Medical Conditions
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21-hydroxylase deficiency
Abdominal aortic aneurysm
ABO blood group
Achondroplasia
Acute lymphoblastic leukemia
Acute myeloid leukemia
Addiction
Addison's disease
Age related macular degeneration
Agenesis of the Corpus Callosum with Peripheral Neuropathy
AIDS
Alcoholism
Allergies
Allograft rejection
Alopecia Areata
Alpha-1 antitrypsin deficiency
Alzheimer's disease
Amyloidosis
Amyotrophic Lateral Sclerosis
Aneurysm
Angioedema
Ankylosing spondylitis
Anorexia nervosa
Anxiety disorder
Arthritis
Asian flush
Asperger syndrome
Asthma
Atherosclerosis
Atopic dermatitis
Atrial fibrillation
Attention deficit hyperactivity disorder
Autism
Autoimmune disease
Autosomal Recessive Spastic Ataxia of Charlevoix-Saguenay
Baldness
Bardet-Biedl syndrome
Basal Cell Carcinoma
Basal cell carcinoma
Behçet's disease
Beta Thalassemia
Bicuspid aortic valve
Bipolar disorder
Bladder cancer
Blood
Blood pressure
Bloom syndrome
Breast cancer
Canavan disease
Cancer
Cancer progression and tumor cell motility
Celiac disease
Central core disease
Cervical cancer
Charcot-Marie-Tooth
Charcot-Marie-Tooth disease
Cholesterol
Chondrodysplasia
Chorionic plate inflammation
Chronic kidney disease
Chronic obstructive pulmonary disease
Cleft palate
Cluster headaches
Colon cancer
Colorblind
Colorectal cancer
Conduct disorder
Congenital adrenal hyperplasia
Coronary artery calcification
Coronary artery disease
Crigler-Najjar syndrome
Crohn's disease
Cystic Fibrosis
Deafness
Deep vein thrombosis
Dementia
Depression
Diabetes
Drug abuse
Dupuytren's contracture
Dyslexia
Dystonia
Earwax
Eczema
Ehlers-Danlos syndrome
Emphysema
Endometrial cancer
Endometriosis
Eosinophilic esophagitis
Epilepsy
Erythropoietic protoporphyria
Factor XI deficiency
Familial dysautonomia
Familial hypercholesterolemia
Familial hypertrophic cardiomyopathy
Familial Mediterranean Fever
Fanconi anemia
Fetal alcohol syndrome
Fibromyalgia
Focal segmental glomerulosclerosis
Food allergy
Frontotemporal dementia
Fuchs' dystrophy
Gallbladder cancer
Gallstone disease
Gastric cancer
Gaucher's disease
GERD
Gestational diabetes
Gilbert syndrome
Glaucoma
Glioma
Glycogen storage disease type 1A
Glycogen storage disease type 1b
Gout
Graves' disease
Hashimoto thyroiditis
HDL cholesterol
Hearing loss
Heart disease
Height
Hemochromatosis
Hemophilia
Hepatitis C
Hereditary fructosuria
Hereditary hemorrhagic telangiectasia type 2
Herpes
High blood pressure
Hirschsprung disease
HIV
Hodgkin lymphoma
Homocystinuria
Hypercholesterolemia
Hyperphenylalaninemia
Hypertriglyceridemia
Hypokalemic periodic paralysis
Hypothyroidism
In vitro fertilization
Inflammatory bowel disease
Intracranial Aneurysm
Intrahepatic cholestasis of pregnancy
Ischemia
Kawasaki disease
Kidney stones
Lactose intolerance
LDL cholesterol
Left
Leprosy
Leukemia
Li-Fraumeni syndrome
Liver cancer
Long QT syndrome
Longevity
Lumbar disc disease
Lung cancer
Lupus
Lyme disease
Lymphoma
Lynch syndrome
Malaria
Male Infertility
Malignant hyperthermia
Malignant melanoma
Maple Syrup Urine Disease
Medium-Chain Acyl-CoA Dehydrogenase Deficiency
Melanoma
Menarche, age at
Meningioma
Mesothelioma
Metabolic syndrome
Migraines
Mucolipidosis type IV
Mucopolysaccharidosis
Multiple myeloma
Multiple sclerosis
Muscular dystrophy
Myasthenia gravis
Myelofibrosis
Myocardial infarction
Myopia
Myotonia congenita
Narcolepsy
Nephrotic syndrome
Neuroblastoma
Nicotine dependence
Niemann-Pick disease
Non-Hodgkin Lymphoma
Nonalcoholic fatty liver disease
Obesity
Obsessive compulsive disorder
Osteoarthritis
Osteoporosis
Otitis
Otosclerosis
Ovarian cancer
Pachyonychia congenita Type I
Pancreatic cancer
Panic disorder
Parkinson disease 8
Parkinson's disease
Pelvic organ prolapse
Pendred Syndrome
Periodontitis
Peripheral arterial disease
Peutz-Jeghers syndrome
Phenylketonuria
Photic sneeze reflex
Pick's disease
Polycystic kidney disease
Polycystic ovary syndrome
Porphyria
Post-traumatic stress disorder
Pre-eclampsia
Premature birth
Primary biliary cirrhosis
Primary hyperoxaluria
Primary sclerosing cholangitis
Progressive supranuclear palsy
Prostate cancer
Pseudoxanthoma elasticum
Psoriasis
Psoriatic arthritis
Resting heart rate
Restless legs syndrome
Retinitis pigmentosa
Rheumatoid Arthritis
Rhizomelic chondrodysplasia punctata type 1
Salla disease
Sarcoidosis
Schizophrenia
Sciatica
Scoliosis
Secondhand smoke susceptibility
Sickle Cell Anemia
Sjogren-Larsson syndrome
Sjögren's syndrome
Skin cancer
SLC22A4 POLYMORPHISM
Smell
Smoking
Social anxiety disorder
Speech
Split hand
Stroke
Sudden Infant Death Syndrome
Suicide
Sun sensitivity
Systemic sclerosis
Taste
Tay-Sachs disease
Testicular cancer
Thiopurine methyltransferase deficiency
Thrombocytopenia
Thyroid cancer
Torsion dystonia
Tourette syndrome
Trimethylaminuria
Tuberculosis
Tuberous sclerosis
Type-1 diabetes
Type-2 diabetes
Tyrosinemia type I
Ulcer
Ulcerative colitis
Ureterolithiasis
Usher syndrome
Venous thromboembolism
Vitamin D Insufficiency
Vitiligo
Von Willebrand disease
Wilson's disease
(hide) 21-hydroxylase deficiency
miscallled by 23andMe, but should indicate being a carrier of allele for congenital adrenal hyperplasia This genotype should indicate being a carrier of Congenital adrenal hyperplasia, but most 23andMe users will find this in their data due to a problem with that testing platform.
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This SNP is supposed to serve as a marker for the Q318X null allele of the 21-hydroxylase gene. This would generally be associated, when homozygous, with the most severe form of congenital adrenal hyperplasia (salt wasting). However, a random survey of 10 publicly uploaded genomes showed all 10 to be carriers. This is well out of Hardy-Weinberg equilibrium, making the accuracy of this SNP as reported by 23andme suspect. Positive results should be clinically correlated and verified in cooperation with your health care provider. [OMIM:?]
4 snps
(hide) Abdominal aortic aneurysm
Slightly lower odds of developing CHD.
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[PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of LDL-C and apolipoprotein B. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): LDL-C: p = 5.2 x 10 (-15);ApoB: p = 7.0 x 10(-18). Type of association: CO; GN] [OMIM:?] [GWAS:LDL cholesterol]
Magnitude: 2
Frequency: 50.0%
Repute:Bad
References:77
Frequency: 50.0%
Repute:Bad
References:77
1.3x risk for Heart Attack. Normal risk for Abdominal Aortic Aneurysm and Brain Aneurysm. One copy of an SNP that increases risk of Myocardial Infarction (Heart Attack) and other Coronary Heart Disease. It has been shown that regularly eating raw vegetables and fruit can reduce the risk to the same level as people without this SNP. This SNP also has the normal medium risk of abdominal aortic aneurysm (weakened artery to abdomen and legs) or brain aneurysm (weakened artery to brain).
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This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...
increased risk for heart disease
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discussed in this blog post as possibly playing a role in coronary heart disease This SNP was also associated with increased risk for coronary artery disease in a Korean population. The association remained significant after adjusting for significant clinical covariates (P=0.001 to 0.024). We identified one risk haplotype (GGGG; P=0.017) and one protective haplotype (AAAA; P=0.007) for development of CAD. Further analysis suggested that the SNPs probably confer susceptibility to CAD in a dominance model (covariates-adjusted P=0.001 to 0.024; OR=2.37 to 1.54). Also found to be significant in a study of 416 Italian myocardial infarction patients. Found to be associated with coronary heart disease in a study of 1360 Chinese Han patients, with an odds ratio of 1.52 (CI: 1.13 - 2.04) for rs2383...
Frequency: 48.7%
References:12
References:12
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discussed in this blog postA region of chromosome 9p21 has revealed numerous SNPs correlated with risk of myocardial infarction in a study of 2,000+ patients. This SNP, rs10116277, is highly correlated (r<sup>2</sup>=0.9) with rs2383207, as well as rs1333040 (r<sup>2</sup>=0.67). Ultimately, though, the SNP in this study (and region) with the highest disease correlation is rs10757278. According to a DeCode report, the G allele of his SNP is associated with lower risk of abdominal aortic aneurysm (AAA). [OMIM:?]
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rs7635818 was associated with abdominal aortic aneurysm (AAA) in an original study population with 502 cases and 736 controls (p = .017) and in an independent replication sample with 448 cases and 410 controls (p = .013; combined p value = .0028; combined odds ratio 1.33). An even stronger association with AAA was observed in a subset of smokers (391 cases, 241 controls, p = .00041, odds ratio 1.80), which represent the highest risk group for AAA. [OMIM:?]
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rs7025486(A) was associated with up to a 20% increased risk of the various vascular diseases, with an odds ratio of 1.21 for abdominal aortic aneurysm (AAA) (p = 4.6x10-10), 1.18 for early onset myocardial infarction (MI) (p = 3.1x10-5), 1.14 for peripheral arterial disease PAD (p = 3.9x10-5), and 1.2 for pulmonary embolism (PE) (p = 00030), but it was not associated with intracranial aneurysm or ischemic stroke. An individual who carried two copies of this allele would have around a 44% increased risk of AAA. No association was seen between the A allele and common risk factors for arterial and venous disease—smoking, lipid levels, obesity, type 2 diabetes, and hypertension. theheart.org DeCode reports that the rs7025486(A;A) genotype is associated with 1.21x odds of peripheral arter...
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rs8003379 is reported to represent a risk factor for abdominal aortic aneurysm (AAA), with odds ratio of 0.41 (CI: 0.26-0.65).
Repute:Bad
References:38
References:38
~1.2x increased risk for heart disease
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rs10757274 is a SNP located in chromosomal region 9p21; to date (2009), it is the strongest genetic predictor of early myocardial infarction (heart attack) discovered so far. SNPs in this region are also associated with increased risk of stroke, abdominal aortic aneurysm (AAA), and intracranial aneurysm. Based on a large (20,000+) study primarily of Caucasian females, it appears that on its own, this single SNP does not improve on the discrimination or classification of predicted heart disease risk achieved by traditional risk factors, high-sensitivity C-reactive protein, and a family history of premature myocardial infarction. rs10757274 and rs2383206 can double the risk of heart diseaseAbout one in every four Caucasians are thought to carry the gene variants. rs10757278] in the same regi...
common in complete genomics
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rs326118 is reported to represent a risk factor for abdominal aortic aneurysm (AAA), with odds ratio of 0.47 (CI: 0.29-0.77).
common in complete genomics appears to be common on the 23andMe platform
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rs1800796 IL-6 572G>C polymorphism (and h.211 haplotype) is associated with abdominal aortic aneurysm (AAA). The risk allele is C. Our results provide evidence that there is a clear genetic influence of IL6 -572C>G polymorphism on plasma levels of fibrinogen and CRP, but this polymorphism does not lead to elevated blood pressure. rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele ...
10 snps
(hide) ABO blood group
Magnitude: 2
O blood group
This genoset defines one of the ABO blood group types, that of type O blood. It is based on the status of the rs8176719 SNP, with the O type predicted by the rs8176719(-;-) genotype.
blood type O
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=Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women. |OA=23andMe blog each copy rs505922(C) is associated with 1.2x risk of pancreatic cancer influences ABO blood group [PharmGKB:Non-Curated GWAS results: Common susceptibility allele are unlikely to contribute as strongly as the FV and ABO loci to VTE risk: results from a GWAS approach. (Initial Sample Size: 419 cases, 1,228 controls; Replication Sample Size: 1,757 cases, 1,480 controls); (Region: 9q34.2; Reported Gene(s): ABO; Risk Allele: rs505922-C); (p-value= 0.000000000000004).This variant is associated with Venous thromboembolism.] [OMIM:?] [GWAS:Venous thromboembolism]
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This SNP is a variant in the ABO gene, and is therefore potentially useful in determining ABO blood group, such as through the use of genosets.
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This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes. Histo-blood group gene polymorphisms as potential genetic modifiers of infection and cystic fibrosis lung disease severity. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. [GWAS:Serum alkaline phosphatase levels]
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This SNP is in the ABO gene, and is therefore potentially useful in determing ABO blood group, such as through the use of genosets.
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This SNP is a variant in the ABO gene, and is therefore potentially useful in determining ABO blood group, such as through the use of genosets.
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This SNP is a variant in the ABO gene, and is therefore potentially useful in determining ABO blood group, such as through the use of genosets.
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ABO blood group rs507666, at the ABO (9q34.2) locus is highly correlated with sICAM-1 concentrations. The novel association at the ABO locus provides evidence for a previously unknown regulatory role of histo-blood group antigens in inflammatory adhesion processes. [PharmGKB:Non-Curated GWAS Results: Novel Association of ABO Histo-Blood Group Antigen with Soluble ICAM-1: Results of a Genome-Wide Association Study of 6,578 Women (Initial Sample Size: 4,570 women; Replication Sample Size: 2,008 women; Risk Allele: rs507666-G). This variant is associated with Soluble ICAM-1.] [GWAS:None] [GWAS:Soluble ICAM-1]
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The T allele of this SNP is associated with higher risk of pancreatic cancer. Phosphodiesterase 8B gene variants are associated with serum TSH levels and thyroid function. Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. Genetic variants associated with Von Willebrand factor levels in healthy men and women identified using the HumanCVD BeadChip. [PharmGKB:Non-Curated GWAS results: Population-based genome-wide association studies reveal six loci influencing plasma levels of live...
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[GWAS:Coagulation factor levels]
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ABO blood group rs8176719 represents a site in the ABO gene, and is a key SNP in determining blood group type O status. An allele that encodes either a blood group type A or type B will have a (G) at this SNP site, i.e. such an allele will be rs8176719(G). If a one-base deletion has occured at this site, removing this nucleotide all together, the corresponding allele is considered to be rs8176719(-) and encodes the most common blood group type O allele. However, an individual will typically only be blood group type O if they are carry two copies of (are homozygous) for this deletion, in other words, if their genotype is rs8176719(-;-). If they carry one copy, they could be blood type A, or blood type B (but are unlikely to be type O). A person who is rs8176719(G;G) is likely to be of blood...
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This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. This particular SNP can be useful in determining whether an ABO type A allele is more specifically an A1 type allele or an A2 type allele. The more common allele (80% of A types on average) is A1, consistent with having a rs8176750(C) allele, with the rarer A2 allele encoded by the deletion form rs8176750(-). This is the key defining characteristic between an A1 and an A2 allele.
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This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. ABO Blood Type [OMIM:?]
Not blood group B
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This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. ABO Blood Type
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This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. ABO Blood Type [OMIM:?] [GWAS:End-stage coagulation]
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This SNP is a variant in the ABO gene, and is therefore potentially useful in determining ABO blood group, such as through the use of genosets. 23andMe reports this as a G/T while decodeme reports it as a an A/C. [PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: Angiotensin converting enzyme activity was increased per copy of the rs8176746 A allele. Carriage of the A allele is associated with the B blood group antigen. Study size: 623 Study population/ethnicity: Academia Sinica Multi-Centered Young-Onset Hypertension (AS-YOH) Genetic Study; Han Chinese individuals with Hypertension. Significance metric(s): p = 9.3 × 10−5 Type of association: PD] [OMIM:?] [GWAS:Hematological and biochemical traits]
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This SNP is in the ABO gene, and is therefore potentially useful in determing ABO blood group, such as through the use of genosets. [GWAS:Tumor biomarkers]
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Influences ABO blood group ABO Blood Type
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Influences ABO blood group ABO Blood Type
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in complete genomics
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may influence ABO blood group see gs129 ABO Blood Type
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Influences ABO blood group ABO Blood Type
1 genoset 22 snps
(hide) Achondroplasia
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Achondroplasia rs121913114
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Achondroplasia? rs267606809
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Achondroplasia rs121913105
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Achondroplasia rs75790268
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs28931614, also known as G380R, Gly380Arg, and c.1138G>A, is a SNP in the fibroblast growth factor receptor 3 FGFR3 gene on chromosome 4. As an autosomal dominant mutation, the rs28931614(A) allele causes achondroplasia, a form of dwarfism. A more rare change at this SNP, c.1138G>C (rather than G>A), also leads to achondroplasia; it is referred to as i6010295 by 23andMe. [OMIM:ACHONDROPLASIA]
5 snps
(hide) Acute lymphoblastic leukemia
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[OMIM:?] [GWAS:Acute lymphoblastic leukemia (childhood)]
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
common/normal
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23andMe blog Acute lymphoblastic leukemia *each rs4132601(G) 1.69x odds of ALL *each rs7089424(G) 1.65x odds of ALL *each rs2239633(G) 1.34x odds of ALL A meta-analysis published in 2014 based on a total of 15 case-control studies with 8333 cases and 36036 controls concluded that rs4132601 was associated with increased ALL risk in Caucasians and Hispanics but not among Asians. [OMIM:?] [GWAS:Acute lymphoblastic leukemia (childhood)]
3 snps
(hide) Acute myeloid leukemia
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rs1131341 (C465T, Arg139Trp) is a snp within NQO1 (NAD(P)H dehydrogenase (quinone 1)). A Trp (T) at this location denotes the NQO1*3 allele. per [pharmgkb], the NQ1*3 allele is associated with reduced enzyme activity T allele strongly associated (OR = 6.36, CI = 1.84 - 21.90, p = 0.002) with infant acute lymphoblastic leukemia among 103 case infants and 185 controls [PharmGKB:Curated T allele causes reduced enzyme activity. May be associated with risk of t-AML and t-MDS. Probably associated with increased risk of ALL;139Arg allele associated with tobacco dose-dependent increase in risk of Head and Neck Squamous Cell Carcinoma.]
1 snp
(hide) Addiction
Magnitude: 3
Frequency: 15.9%
Repute:Bad
References:102
Frequency: 15.9%
Repute:Bad
References:102
higher risk for nicotine dependence, lower risk for cocaine dependence
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Associated with smoking phenotype (p=0.007) based on association study of 2,000+ individuals, and functional studies demonstrated that the risk allele decreased response to a nicotine agonist, therefore the rs16969968(A) allele is likely to be involved in nicotine dependence. In a study 500+ individuals with cocaine dependence, the same rs16969968(A) allele was associated with a 0.67x decreased risk (p = 0.0045). A study of 200 individuals replicated the association between this SNP and nicotine dependence, and also concluded that the rs16969968(A) allele was significantly associated with 'enhanced pleasurable responses' to a person's first cigarette. 23andMe blog 23andMe considers rs1051730 equivalent The association between rs16969968 and lung cancer may, in part, be confounded by chroni...
A1/A2: Bad at avoidance of errors. 0.5x lower OCD risk, 0.87x lower Tardive Diskinesia risk, higher ADHD risk. More Alcohol Dependence. Lower risk of Postoperative Nausea. Increased obesity. Bupropion is not effective. The DRD2 TaqIA A1/A2 version causes less dopamine receptors. Doesn't learn from mistakes well. Reduced response to errors and increased addictive behavior Men may have half the risk of Obsessive Compulsive Disorder but higher risk of ADHD. Women have lower Persistence. 0.87x reduced risk of Tardive Diskinesia when taking dopamine receptor antagonists. Slightly increased risk of alcoholism and smoking addiction. Slower recovery from traumatic brain injury. Lower risk of postoperative nausea within 6 hours of surgery. Bupropion (Wellbutrin, Budeprion, Prexaton, Elontril, Aple...
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain . Reduced response to errors and increased addictive behavior It has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessa...
1.8x increased risk of lung cancer; reduced response to alcohol, therefore possibly increased risk of alcohol abuse
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rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...
Magnitude: 2.5
Frequency: 20.0%
Repute:Bad
References:9
Frequency: 20.0%
Repute:Bad
References:9
1.28x lung cancer risk
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rs17487223 increases susceptibility to Lung cancer 1.28 times for carriers of the T allele plos Risk Factors for Age-Dependent Nicotine Addiction
Increased risk of Nicotine dependence among males
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associated with vulnerability to nicotine addiction in men. g2b2mh blog rs1044396 mediates effects of nicotine self-medication via parietal cortex. subjects with the (T;T) genotype showed robust brain activity in the parietal cortex while subjects with the (C;C) genotype showed very little change in activity. [PharmGKB:Curated This variant is closely linked to rs2236196 and has been associated with the intensification of nicotine dependence.] [OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 4; CHRNA4]
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Along with rs6442925 and rs534654, this SNP, rs1534891, is part of a 3-SNP (multi-locus) interaction that is associated with bipolar disorder.
1.3x increased risk for alcoholism
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rs1076560 is located in intron 6 of the dopamine receptor D2 gene. In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism. rs1076560 and the DAT 3'-VNTR variant influences memory Genetic variants altering dopamine D2 receptor expression or function modulate the risk of opiate addiction and the dosage requirements of methadone substitution [PharmGKB:Curated This variant is a potential marker for alcoholism. A allele was more prevalent in the alcoholic patients than in the healthy controls in a study consists of 248 alcohol...
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Only for Hispanics, individuals who have a genoset composed of rs1799913(C;C) and rs4290270(T;T) are reported to be at 9x higher risk for developing heroin addiction (CI:0.83-244.63, p=0.012).
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated A study on 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry found first evidence for the involvement of DDC in the susceptibility to nicotine dependence. This variant in the DDC gene is part of t...
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated In a total of 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry, this SNP in the DDC gene was significantly associated with two of the three adjusted nicotine dependence measures in the European-A...
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Heroin addiction in African Americans: a hypothesis-driven association study.
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated A study on 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry found first evidence for the involvement of DDC in the susceptibility to nicotine dependence. This variant in the DDC gene is part of t...
1.4x higher schizophrenia risk
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rs6277 (957C>T, Pro319Pro) is one of several SNPs in the dopamine receptor DRD2 gene. In a study of 300+ Russian patients with schizophrenia, the rs6277(C) allele was associated with higher risk. From a pooled meta-study (total of 4 other reports plus this one) the allelic odds ratio is 1.42 (CI: 1.26-1.61, p<0.00005), and the genotypic odds ratio for the (C;C) genotype was 1.6 (CI: 1.32-1.95, p<0.00005). Note that rs6275 and rs6277 are only 18bp apart, hence their very tight linkage (r<sup>2</sup>=1). gs278 reflects a gene-gene interaction between this SNP and a NR3A SNP, rs10989591, in which older adults with a particular combination of genotypes at these two (independent) loci are reported to exhibit better episodic memory. C allele associated significantly (p = 0.0...
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Implicated as part of a haplotype of the dopamine D1 receptor DRD1 gene associated with autism spectrum disorders in families having only affected males. The haplotype is rs265981(C)-rs4532(A)-rs686(T) as published, though not necessarily as oriented in dbSNP. [OMIM:DOPAMINE RECEPTOR D1; DRD1]
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Implicated as part of a haplotype of the dopamine D1 receptor DRD1 gene associated with autism spectrum disorders in families having only affected males. The haplotype is rs265981(C)-rs4532(A)-rs686(T) as published, though not necessarily as oriented in dbSNP. Significant association of DRD1 with nicotine dependence. A haplotype of the DRD1 gene is associated with alcohol dependence. The influence of serotonin- and other genes on impulsive behavioral aggression and cognitive impulsivity in children with attention-deficit/hyperactivity disorder (ADHD): Findings from a family-based association test (FBAT) analysis. Differential allelic expression of dopamine D1 receptor gene (DRD1) is modulated by microRNA miR-504. Heroin addiction in African Americans: a hypothesis-driven association study....
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This SNP is associated with opioid dependence and addiction in females. The risk allele is the minor allele, rs1022563(T).
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commonly referred to as A779C Only for Hispanics, individuals who have a genoset composed of rs1799913(C;C) and rs7963720(T;T) are reported to be at 14x higher risk for developing heroin addiction (CI:0.83-244.63, p=0.012). Again, only for Hispanics, individuals having a genoset composed of rs1799913(C;C) and rs4290270(T;T) are reported to be at 9x higher risk for developing heroin addiction (CI:0.5-153, p=0.063). Association between 5-HT2A, TPH1 and GNB3 genotypes and response to typical neuroleptics: a serotonergic approach. Tryptophan hydroxylase gene 1 (TPH1) variants associated with cerebrospinal fluid 5-hydroxyindole acetic acid and homovanillic acid concentrations in healthy volunteers. [OMIM:TRYPTOPHAN HYDROXYLASE 1; TPH1]
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In 2009, a large, multi-sample replication study failed to find any significant association with Intelligence for this or other SNPs in CHRM2 . Earlier work had observed that this snp (and perhaps its neighbors) influenced intelligence and alcohol dependence CHRM2 gene predisposes to alcohol dependence, drug dependence and affective disorders: results from an extended case-control structured association study. And the earlier and or this pdf poster show association between the CHRM2 gene and intelligence . In this study of ~300 Caucasians, the (T;T) genotype appeared to typically have a 4 point higher IQ than the (A;T) genotype, which had a 4 point higher IQ (on average) than the (A;A) genotype. A nearby SNP, rs324640, showed similar results to rs324650, and was in linkage disequilibrium (...
normal
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rs4648317, a SNP in the dopamine D2 receptor DRD2 gene, has been linked to higher rates of smoking and higher nicotine dependence scores, based on a study of ~220 adolescents. The risk allele rs4648317(T).
Magnitude: 0
Frequency: 84.1%
Repute:Good
References:8
Frequency: 84.1%
Repute:Good
References:8
common in complete genomics
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[PharmGKB:Curated This promoter variant affects total DRD2 mRNA expression. The C allele is associated with enhanced total DRD2 mRNA expression and is associated with working memory activity in prefrontal cortex and striatum of schizophrenia patients.]
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Association between ADORA2A and DRD2 polymorphisms and caffeine-induced anxiety. Physiogenomic analysis of localized FMRI brain activity in schizophrenia. Evaluation of genetic variability in the dopamine receptor D2 in relation to behavioral inhibition and impulsivity/sensation seeking: an exploratory study with d-amphetamine in healthy participants. Pharmacogenetics and antipsychotics: therapeutic efficacy and side effects prediction. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: Having the AA genotype of this variant was associated with a protective effect from increased prolactin concentration. Study size: 90. Study population/ethnicity: 7-17-year-old patients chronically treated with risperidone; non-Hispanic Caucasians. Significance metric(s): p = 0.002. Type ...
25 snps
(hide) Addison's disease
Frequency: 59.5%
Repute:Bad
References:11
Repute:Bad
References:11
slightly increased risk for several autoimmune diseases
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rs12150220 is a SNP in the NLRP1 gene, which encodes the NACHT leucine-rich-repeat protein 1. SNPs in this gene may be involved in higher risk for several autoimmune diseases. In a study investigating large patient cohorts from six different autoimmune diseases, including autoimmune Addison's disease (n=333 patients), type-1 diabetes (n=1086), multiple sclerosis (n=502), rheumatoid arthritis (n=945), systemic lupus erythematosus (n=156) and juvenile idiopathic arthritis (n=505), plus 3273 healthy controls, the rs12150220(A) allele was associated with higher risk for both autoimmune Addison's disease (odds ratio 1.25, CI: 1.06-1.49, p = 0.007) and type-1 diabetes (odds ratio 1.15, CI: 1.04-1.27, p = 0.005). [OMIM:NLR FAMILY, PYRIN DOMAIN-CONTAINING 1; NLRP1]
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
2 snps
(hide) Age related macular degeneration
2.5x risk for AMD; higher mortality among nonagenarians To minimize your risk of age related macular degeneration, consider a diet rich in vitamins C and E, lutein, zeaxanthin and the minerals zinc and copper, such as kale, spinach and broccoli. source
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rs1061170 is a SNP in the complement factor H CFH gene; it is also known as Tyr402His. The rs1061170(T) allele encodes the more common Tyr (Y), while the generally rarer rs1061170(C) encodes the His (H). This SNP has been associated primarily with age related macular degeneration, and to a lesser extent, with longevity. This research paper shows that CFH Y402H is the relevant mutation. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD. rs1061170 (aka Y402H 1277 T>C) was not associated with exudative AMD. CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese CFH variant rs1061170 Y402H is strongly associated with both dry and wet AMD rs1061170(C) alleles are significantly associa...
3.9x increased risk of wet ARMD age related macular degeneration
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rs1136287, also known as Met72Thr, is a SNP in the PEDF gene. Analysis of 86 Taiwanese Chinese patients with wet age related macular degeneration (ARMD) found the (T) allele to be more frequent in patients than in controls (50% vs 31%; p =.0005). The rs1136287(T;T) genotype was also more prevalent in patients than in controls (odds ratio 3.9, p = .0015).
common but higher risk of age related macular degeneration
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rs3775291 is a SNP in the TLR3 gene associated with an amino acid change in the corresponding protein. In the orientation as shown in dbSNP, the more common rs3775291(G) allele encodes a leucine while the rarer rs3775291(A) allele encodes a phenylalanine. rs3775291 has been associated with one form of age related macular degeneration (ARMD), specifically, the form known as 'dry' ARMD, also known as geographic atrophy. A study of 3 case-control groups of Americans of European descent, comprising about 900 ARMD patients in total, indicated that having one rs3775291(A) allele reduces the odds of having dry ARMD about 30%, and being a rs3775291(A;A) homozygote cuts your odds by more than half. Specifically, the odds ratio of having dry ARMD with one minor allele is 0.712 (CI: 0.50-1.0), and fo...
1.5x risk for ARMD
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rs3793784, a SNP upstream of the ERCC6 DNA repair gene, has been linked independently and in conjunction with another SNP (rs380390) to age related macular degeneration. On it's own, the odds ratios for increased risk for heterozygotes and homozygotes, were, respectively, 1.51 (CI 1.07-2.11) and 1.60 (CI 0.99-2.61). In dbSNP orientation, individuals who are CFH gene SNP genotype rs380390(C;C) and are also rs3793784(G;G) for this (ERCC6) SNP are calculated to be at 23 fold higher risk for developing age related macular degeneration compared to individuals who are homozygous for the more common alleles (among Caucasians) at both loci (ie who are rs380390(G;G) and rs3793784(C;C). Genetic markers and biomarkers for age-related macular degeneration. ERCC6/CSB gene polymorphisms and lung cancer ...
5% higher risk of Age related macular degeneration
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rs800292 is a SNP in the complement factor H CFH gene; it has been linked to blindness in age related macular degeneration. This SNP is also known as 184G>A, I62V, or Val62Ile. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese A study of Chinese AMD patients reports that carriers of both rs11200638 and rs800292 risk alleles pushes the odds ratio for AMD up to 23x. Overall, an 'extremely high' population attributable risk (PAR) of 78% reported for these SNPs. rs800292 was associated with polypoidal choroidal vasculopathy (PCV) in a study of 130 Japanese patients. age related macular degeneration Susceptibility genes for age-re...
slightly higher risk for Alzheimers in Caucasians but not Asians This variant has been reported to be associated with a slightly higher risk for Alzheimers disease in Caucasians but not in Asians.
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rs1064039, also known as G73A, Ala25Thr or A25T, is a variant in the cystatin C CST3 gene. A relatively small study (167 patients) concluded that rs1064039(A;A) genotypes had about a 3 fold increase in risk for exudative age-related macular degeneration (ARMD). A meta-analysis of 2,410 cases and 2,539 controls reported that although the rs1064039(A) allele is associated with about a 1.5x increased odds ratio for developing Alzheimer's disease in Caucasians, no increased risk was seen in Asians. [OMIM:?]
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[GWAS:Age-related macular degeneration]
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[GWAS:Age-related macular degeneration]
Frequency: 30.1%
References:9
References:9
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Plasma complement components and activation fragments: associations with age-related macular degeneration genotypes and phenotypes. Genetic analysis of typical wet-type age-related macular degeneration and polypoidal choroidal vasculopathy in Japanese population. [OMIM:MACULAR DEGENERATION, AGE-RELATED, 1; ARMD1] [GWAS:Age-related macular degeneration]
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[GWAS:Age-related macular degeneration]
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[GWAS:Age-related macular degeneration]
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linked to blindness in old age rs3753394 carries a significantly increased risk for exudative AMD. linked to rs3753394, rs800292, rs1061147, rs1061170, rs380390, and rs1329428 Significant associations were detected for AMD with rs3753394 rs800292 rs1329428 A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese Multiple gene polymorphisms in the complement factor h gene are associated with exudative age-related macular degeneration in chinese. Plasma therapy in atypical haemolytic uremic syndrome: lessons from a family with a factor H mutation. Association analysis of CFH, C2, BF, and HTRA1 gene polymorphisms in Chinese patients with ...
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[GWAS:Age-related macular degeneration]
Frequency: 40.7%
References:2
References:2
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[GWAS:Age-related macular degeneration]
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age related macular degeneration [OMIM:COMPLEMENT FACTOR H-RELATED 3; CFHR3] [GWAS:Age-related macular degeneration]
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age related macular degeneration
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[GWAS:Age-related macular degeneration]
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[GWAS:Age-related macular degeneration]
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age related macular degeneration
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[GWAS:None]
None
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linked to blindness in old age rs3753394, rs800292, rs1061147, rs1061170, rs380390, and rs1329428 CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese [PharmGKB:Non-Curated GWAS Results: Complement factor H polymorphism in age-related macular degeneration (Initial Sample Size: 96 cases, 50 controls; Replication Sample Size: NR; Risk Allele: rs380390-C).] [OMIM:EXCISION-REPAIR CROSS-COMPLEMENTING, GROUP 6; ERCC6] [GWAS:Age-related macular degeneration]
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[GWAS:Age-related macular degeneration]
Frequency: 48.7%
References:9
References:9
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[OMIM:COMPLEMENT FACTOR H-RELATED 3; CFHR3] [GWAS:Age-related macular degeneration]
?
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linked to blindness in age related macular degeneration rs3753394, rs800292, rs1061147, rs1061170, rs380390, and rs1329428 Significant associations were detected for AMD with rs3753394 rs800292 rs1329428 A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese [GWAS:None]
Normal 0.97x risk for Age Related Macular Degeneration. When the retina cells in the eye get damaged with age, it is known as Age Related Macular Degeneration. This SNP has about the average risk. The SENS Research Foundation is working on a promising cure for Age Related Macular Degeneration: http://www.sens.org/outreach/conferences/lysosens-synthetic-biology-approach-treat-age-related-macular-degeneration
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may influence age related macular degeneration (damage to the eye with ageing) when part of the haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC), but does not appear to do so alone. age related macular degeneration [GWAS:Age-related macular degeneration]
Frequency: 53.6%
References:4
References:4
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analysis of a published data set on age related macular degeneration revealed an unreported haplotype near rs10272438 (P value = 0.0024).
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nature age related macular degeneration is associated with five highly correlated SNPs (rs10490924, rs3750848, rs3793917, rs11200638 and rs932275; r2 < 0.88) showed strongest association with AMD (2.72 < OR < 2.86) Cigarette smoking strongly modifies the association of LOC387715 and age-related macular degeneration. A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration. Genetic and functional dissection of HTRA1 and LOC387715 in age-related macular degeneration. Genetic analysis of typical wet-type age-related macular degeneration and polypoidal choroidal vasculopathy in Japanese population. [GWAS:Age-related macular degeneration (extreme sampling)]
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association with ARMD Common variation in three genes, including a noncoding variant in CFH, strongly influences risk of age-related macular degeneration. CFH, ELOVL4, PLEKHA1 and LOC387715 genes and susceptibility to age-related maculopathy: AREDS and CHS cohorts and meta-analyses. A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration. Cigarette smoking strongly modifies the association of LOC387715 and age-related macular degeneration. Rapid inexpensive genome-wide association using pooled whole blood. Genetic and functional dissection of HTRA1 and LOC387715 in age-related macular degeneration. Genome-wide association study identifies two susceptibility loci for exudative age-related macular degeneration in the Japanes...
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[GWAS:Age-related macular degeneration]
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age related macular degeneration
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nature age related macular degeneration is associated with five highly correlated SNPs (rs10490924, rs3750848, rs3793917, rs11200638 and rs932275; r2 < 0.88) showed strongest association with AMD (2.72 < OR < 2.86) A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration. Genetic and functional dissection of HTRA1 and LOC387715 in age-related macular degeneration. An intergenic region between the tagSNP rs3793917 and rs11200638 in the HTRA1 gene indicates association with age-related macular degeneration. Association between high-risk disease loci and response to anti-vascular endothelial growth factor treatment for wet age-related macular degeneration. Association of genetic polymorphisms and age-related macular d...
normal
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news rs2511989 not associated with AMD rs2511989(A;A) had a protective effect against age related macular degeneration. Comparison of the rs2511989(A;G) genotype and the wild type (G;G) genotype yielded an odds ratio of 0.63 (CI: 0.47 to 0.84) for age-related macular degeneration. Comparison of rs2511989(A;A) homozygotes with (G;G) homozygotes resulted in an odds ratio of 0.44 (CI: 0.31 to 0.64). [PharmGKB:Curated A case-control study in a UK sample of 479 patients with age-related macular degeneration and 479 controls identified a highly significant association of this variant in intron six of the SERPING1 gene with age-related macular degeneration.]
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T allele is associated with 3.47mg/dl increase in HDL cholesterol (good cholesterol). [PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of HDL-C and apolipoprotein A1. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): HDL-C: p = 1.0 x 10 (-41);ApoA1: p = 1.1 x 10(-34). Type of association: CO; GN] [OMIM:?] [GWAS:HDL cholesterol]
Magnitude: 0
Frequency: 61.1%
Repute:Good
References:58
Frequency: 61.1%
Repute:Good
References:58
normal
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rs10490924 was identified as a risk factor from chromosome 10 related to age related macular degeneration. The risk allele is (T). Odds ratios for heterozygotes and homozygotes are, respectively, 2.69 (CI: 2.22-3.27) and 8.21 (CI: 5.79-11.65). Disease risk in combination with the rs1061170 SNP in the CFH gene is dramatically increased. Homozygotes for both the rare/risk alleles at both loci are estimated to be at 57 fold higher risk for age related macular degeneration than individuals homozygous for the common alleles at both loci. A subsequent study indicated that the risk based on solely the ARMS2 SNP rs10490924 is significantly higher in smokers than in non-smokers. Based on a study of ~750 patients, rs10490924 is significantly higher in participants with choroidal neovascularization t...
Normal/Average risk for Alzheimer's
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Apolipoprotein E ApoE status is technically defined by two different SNPs, rs429358 and rs7412. This SNP, rs4420638, is situated about 14kb away in the adjacent ApoC1 gene and is co-inherited with ApoE and thus associated with late-onset Alzheimer's disease. rs4420638 (the proxy SNP) is not independent of rs429358. These two SNPs are correlated with each other and it's believed that most of the association with AD at rs4420638 is due to its proximity to rs429358. That said, rs4420638 is not a perfect proxy for rs429358 either -- rs4420638 correlates better for certain genotypes and for certain ethnicities. For example, if you have the genotype at rs4420638 that is more correlated with the e4 allele of APOE, you still only have a 50% chance of actually having the e4 allele. And rs4420638 is...
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age related macular degeneration
common on affy axiom data
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rs3732378 VAL249ILE is tightly linked to neighboring rs3732379 THR280MET The protein receptor with both variant amino acids is known as CX3CR1-M280. the minor alleles of this pair are associated with *more rapid progression to full-blown AIDS and probably increased susceptibility to HIV infection *reduced risk of acute coronary events *increased risk of age related macular degeneration [OMIM:?]
normal http://www.diygenomics.org/webapp/gen_data.php
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Located close to ApoE4, yet may independently (also) influence risk of Alzheimer's disease. A case-control study of 381 patients found a 2x higher risk for Alzheimer's disease associated with the rarer rs2075650(G) allele. This allele is associated with earlier onset of Alzheimer's disease, by ~7 years. (news) The data from this study are available online at The association of this SNP with late-onset Alzheimer's disease] was confirmed by a study reported in PLoS Genetics. The A allele of this SNP is one of 150 identified as relevant to exceptional longevity in Recent work suggests, however, that the linkage disequilibrium between rs2075650 and the ApoE ε4 defining SNP rs429358 means that there may be little, if any, independent effect of rs2075650 on Alzheimer's risk. rs2075650] was ...
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age related macular degeneration A forest-based approach to identifying gene and gene gene interactions. Neovascular age-related macular degeneration risk based on CFH, LOC387715/HTRA1, and smoking. Plasma therapy in atypical haemolytic uremic syndrome: lessons from a family with a factor H mutation. Association of factor H autoantibodies with deletions of CFHR1, CFHR3, CFHR4, and with mutations in CFH, CFI, CD46, and C3 in patients with atypical hemolytic uremic syndrome. A particle swarm based hybrid system for imbalanced medical data sampling. Complement component 3: an assessment of association with AMD and analysis of gene-gene and gene-environment interactions in a Northern Irish cohort.
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age related macular degeneration Haplotypes in the complement factor H (CFH) gene: associations with drusen and advanced age-related macular degeneration. Three major loci involved in age-related macular degeneration are also associated with polypoidal choroidal vasculopathy.
common in clinvar
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age related macular degeneration [OMIM:COMPLEMENT FACTOR B; CFB] [GWAS:Age-related macular degeneration]
Magnitude: 0
Frequency: 86.7%
Repute:Good
References:1
Frequency: 86.7%
Repute:Good
References:1
common in complete genomics
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association with age-related macular degeneration (ARMD) risk allele said to be (A), in dbSNP orientation (ref: Navigenics apparently uses rs522162] as a proxy (substitute) for rs641153 [GWAS:Age-related macular degeneration]
common in complete genomics
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rs547154 significantly associated with Age-related maculopathy in both our case-control (P-value 0.00007) and family data (P-value 0.00001). [OMIM:COMPLEMENT COMPONENT 2 DEFICIENCY]
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[GWAS:Age-related macular degeneration]
common in clinvar
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rs1047286 is a SNP in the complement component C3 gene. A 2011 meta-analysis of seven studies concluded that, at least for Caucasians, the rs1047286(C;T) and (T;T) genotypes had 1.27 (CI: 1.15 - 1.41) and 1.70 (CI: 1.27 - 2.11) times higher risk of ARMD than did (G;G) genotypes. [OMIM:C3 POLYMORPHISM, HAV 4-1 PLUS/MINUS TYPE]
Magnitude: 0
Repute:Good
References:75
Repute:Good
References:75
normal
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rs11200638, a SNP in the HTRA1 promoter, is associated with a 10 fold increased risk of wet age related macular degeneration in Japanese and Caucasian populations. Further confirmed . The genotype at highest risk is (A;A). Note, most studies have shown that that this SNP is highly predictive (i.e. is in near perfect (D'>0.98) linkage disequilibrium) with rs10490924, thus the status of one very closely predicts the status of the other. However, one Caucasian AMD study reported the linkage disequilibrium measure for these two SNPs on 10q26, (i.e., rs10490924, which is upstream of HTRA1 in LOC387715/ARMS2, and rs11200638) as D'=0.8, and all four possible haplotypes of the two SNPs were detected in the samples. Further, this same study reported that these two SNPs appear to contribute equal...
normal
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rs3025039, also known as the +936C/T SNP in the VEGFA gene, has been associated with age-related macular degeneration (ARMD). A study of 190 Taiwanese patients with late wet age related macular degeneration found that the rs3025039(T) allele was associated with increased risk, with an odds ratio of 2.61 (CI: 1.68 to 4.07, p = 1.45 x 10e-5). Note that this association may be completely due to the tight linkage (D' = 0.99) between this SNP and rs1061170, which has been reported by numerous studies to be associated with ARMD. C->T was associated with increased risk for altitude sickness. Vascular endothelial growth factor gene polymorphisms in Behcet's disease. Polymorphisms in the vascular endothelial growth factor gene and breast cancer in the Cancer Prevention Study II cohort. Vascular ...
common
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rs2230199, a SNP in the complement component C3 gene, has been reported by several investigators to be associated with ARMD. The common allele at this SNP is known as Arg102; the variant and risk allele is known as Gly102. The risk allele, in orientation to the dbSNP entry for this rs#, is (G). In one of the largest case-control studies, the odds ratio associated with heterozygotes is 1.61, and for homozygotes, 3.26 (p = 4.5 x 10e-12). NEJM reports significant associate with ARMD. blog post [PharmGKB:Curated rs2230199 was found to be associated with risk of age-related macular degeneration in English and Scottish case-control studies.] [OMIM:MACULAR DEGENERATION, AGE-RELATED, 9; ARMD9] [GWAS:Age-related macular degeneration]
common in clinvar
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age related macular degeneration [OMIM:COMPLEMENT FACTOR B; CFB]
normal
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age related macular degeneration Genetic markers and biomarkers for age-related macular degeneration. C2 and CFB genes in age-related maculopathy and joint action with CFH and LOC387715 genes. Analysis of rare variants in the complement component 2 (C2) and factor B (BF) genes refine association for age-related macular degeneration (AMD). Variations in five genes and the severity of age-related macular degeneration: results from the Muenster aging and retina study. Multilocus analysis of age-related macular degeneration. Plasma complement components and activation fragments: associations with age-related macular degeneration genotypes and phenotypes. Complement component 3: an assessment of association with AMD and analysis of gene-gene and gene-environment interactions in a Northern Irish...
53 snps
(hide) Agenesis of the Corpus Callosum with Peripheral Neuropathy
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Agenesis of the Corpus Callosum with Peripheral Neuropathy (ACCPN) rs121908428
2 snps
(hide) AIDS
60% reduction in HIV viral load The rs9264942(C;T) genotype is reported to be associated with a 60% reduction in viral load in HIV-infected individuals. See also rs9264942 and HIV.
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This SNP (C/T) is in 5' region of the HLA-C gene, 35 kb away from transcription initiation in or around the HLA-C gene. 'People with this tiny sequence variation, dubbed rs9264942, appear to have up to 90% less virus in their systems than those who carry other polymorphisms. About 10% of Europeans appear to carry two copies of rs9264942, which leads to an average 90% viral load reduction. About 50% of Europeans carry one copy, which gives a 60% reduction. By comparison, less than 40% of people of African descent appear to carry a single copy of the polymorphism.' Genetic variation may lower HIV load by 90% They are referring to the (C;C) genotype giving a 90% reduction and the (C;T) giving a 60% reduction. dbSNP page This SNP is also reported to account for 6.5% of the 15% variation in vir...
complex; generally greater risk for cancer progression
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rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and H131R. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...
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[GWAS:AIDS]
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[GWAS:AIDS]
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shows that the following four SNPs in the MHC region play a particular important role in the protection of developing AIDS: rs9264942, rs4418214, rs2395029, rs3131018 also including the two variants in CCR5 rs333 (delta32) and C927T.
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[GWAS:AIDS]
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[GWAS:AIDS]
common, but faster HIV progression
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23andMe blog females with one copy of rs5968255(C) progressed from HIV infection to AIDS more slowly with an average of eight years, nearly four times more than females with no copies or males. The search for host genetic factors of HIV/AIDS pathogenesis in the post-genome era: progress to date and new avenues for discovery. Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations? HIV Progression
common in clinvar
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Compared with individuals without CCR5-Delta32 (a variation in another gene) or rs1799864(A), individuals with one or two copies of rs1799864(A) had a 58% lower risk of developing AIDS during the first 4 years after testing positive for HIV, a 19% lower risk during the subsequent 4 years, and no significant protection thereafter. No protective effect (ie no benefit) was seen for this SNP once AIDS had developed. rs1799864(G), rs3025058(A) and rs662 were associated with increased risk, and rs1800775(A) with reduced risk of recurrent venous thromboembolism [OMIM:HUMAN IMMUNODEFICIENCY VIRUS TYPE 1, RESISTANCE TO]
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[GWAS:AIDS]
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:2
Frequency: 85.8%
Repute:Good
References:2
common The rs2395029(T;T) genotype is the common genotype for this SNP, against which the rs2395029(T;G) and rs2395029(G;G) genotypes that are associated with reduced HIV viral load in HIV carriers are compared. See also rs9264942 and HIV.
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rs2395029 is a SNP in the major histocompatibility complex (MHC) region, and several studies have shown that the rs2395029(G) allele is 99.9% predictive of the presence of an HLA-B*5701 allele. This HLA allele, in turn, has been associated with several conditions. A study of 51 cases of flucloxacillin drug-induced liver injury (DILI), an important cause of serious liver disease, along with a replication study of another 23 cases, found that the rs2395029(G) carriers were at highly increased risk (odds ratio 80, p=8.7x10(-33)). * see also: 23andMe blog rs2395029(G;G) increases the odds of drug-induced liver injury in response to flucloxacillin by 45x This SNP is thought to be involved in determining the HIV viral load set point during the asymptomatic period of infection. This SNP is estima...
not resistant to HIV
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this snp is on the 23andMe microarray but lacks a dbSNP identifier. discussed in the 23andMe blog *II +/+: Not resistant to HIV infection; shows average time of progression to AIDS after infection. *DI Delta32/+: Not resistant to HIV infection but may have slower progression to AIDS after infection. *DD Delta32/Delta32: Resistant to infection by the most common strain of HIV people usually encounter, though protection is not complete. Article also seems to discuss rs333 (aka CCR5Delta32) Resistance to HIV/AIDS
13 snps
(hide) Alcoholism
A1/A2: Bad at avoidance of errors. 0.5x lower OCD risk, 0.87x lower Tardive Diskinesia risk, higher ADHD risk. More Alcohol Dependence. Lower risk of Postoperative Nausea. Increased obesity. Bupropion is not effective. The DRD2 TaqIA A1/A2 version causes less dopamine receptors. Doesn't learn from mistakes well. Reduced response to errors and increased addictive behavior Men may have half the risk of Obsessive Compulsive Disorder but higher risk of ADHD. Women have lower Persistence. 0.87x reduced risk of Tardive Diskinesia when taking dopamine receptor antagonists. Slightly increased risk of alcoholism and smoking addiction. Slower recovery from traumatic brain injury. Lower risk of postoperative nausea within 6 hours of surgery. Bupropion (Wellbutrin, Budeprion, Prexaton, Elontril, Aple...
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain . Reduced response to errors and increased addictive behavior It has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessa...
apparently more prone to alcoholism interacts with the medicine Finasteride
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This SNP in the GABRA2 gene has been linked to Alcoholism. The effect of this SNP, a synonymous change at amino acid residue 132, is unknown, but it does not change the GABRA2 protein sequence. Carriers of at least one rs279858(G) allele respond slower to the effects of alcohol and are thereby apparently more prone to alcoholism than carriers of two rs279858(A) alleles. Finasteride, an FDA approved drug for the treatment of benign prostatic hypertrophy and a modulator of GABRA2, was shown to have more of a blocking effect on rs279858(A) homozygotes. Note that nearby SNPs have been grouped into a haplotype that shows statistically stronger association with alcohol dependence, namely the haplotype consisting of the rs279871(A) + rs279845(T) + rs279836(A) alleles . 1050 nicotine-dependent cas...
topiramate may work to reduce heavy drinking best for this genotype Research by Dr. H. Kranzler's group has found that the drug topiramate was more effective in reducing heavy drinking in individuals with this rs2832407(C;C) genotype.
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The rs2832407(C) allele has inconsistently been linked to alcoholism and its treatment. Nonetheless, a 2014 report based on 138 patients concludes that rs2832407(C;C) individuals show a greater decrease than non-carriers (of a rs2832407(C) allele) in the number of heavy drinking days per week when taking topiramate at a dose of 200 mg/daily. A follow-up study done 3 and 6 months after treatment seemed to mostly confirm the topiramate benefit preferentially to rs2832407(C;C) individuals.
2x risk of severe alcohol withdrawal. Possible increased odds of ADHD. Alcoholics with this are twice as likely to have seizures during alcohol withdrawal.
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rs27072, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27048. The rs27072 polymorphism has been shown to be significantly associated with ADHD in clinical samples of Canadian children aged 6 to 16 [Feng et al., 2005] and the significant association was also reported by Ouellet-Morin et al. in a Canadian twin study, 2008 (Am. J. of Medical Genetics Part B, 147B:1442-1449 (2008). The interaction between the dopamine transporter gene and age at onset in relation to tobacco and alcohol use among 19-year-olds. Association of promoter variants of human dopamine transporter gene with schiz...
Alcohol Flush: Normal, doesn't flush. Normal hangovers. Normal risk of Alcoholism. Normal risk of Esophageal Cancer. Disulfiram is effective for alcoholism. Two working copies of Aldehyde Dehydrogenase (ALDH2) mean you won't turn bright red when you drink alcohol, unlike most Asians. After your body turns alcohol into the dangerous acetaldehyde, this gene quickly turns the acetaldehyde into vinegar. It also stops the acetaldehyde in cigarettes from causing Esophageal Cancer. It reduces hangovers compared to Asians, but less hangovers and flushing obviously increases the risk of alcoholism. Alcoholism can be treated effectively with the drug Disulfiram (Antabuse) which would stop this gene from working and cause the Asian flush in non-Asians. PMC2659709 [http://www.ncbi.nlm.nih.gov/pmc/art...
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rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Disulfiram (...
normal oral/throat cancer risk; more frequent alcohol consumption
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A SNP in rs1229984 encodes a form of the alcohol dehydrogenase ADH1B gene that significantly reduces the clearance rate of alcohol from the liver. This SNP is also known as Arg48His, with the (G) allele corresponding to the Arg and the (A) to the His. Known in the literature as ADH2*2 or sometimes ADH1B*2, the allele with increased activity (meaning more rapid oxidation of ethanol to acetaldehyde) is His48, encoded by rs1229984(A). Individuals with one or especially two ADH2*2 alleles, ie genotypes rs1229984(A;G) or rs1229984(A;A) are more likely to find drinking unpleasant and have a somewhat reduced risk for alcoholism. A study of over 3,800 cases of 'upper aerodigestive' cancers (mouth/throat, voice box, and esophageal cancers) concluded that the rs1229984(A) allele (in dbSNP orientatio...
1.3x increased risk for alcoholism
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rs1076560 is located in intron 6 of the dopamine receptor D2 gene. In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism. rs1076560 and the DAT 3'-VNTR variant influences memory Genetic variants altering dopamine D2 receptor expression or function modulate the risk of opiate addiction and the dosage requirements of methadone substitution [PharmGKB:Curated This variant is a potential marker for alcoholism. A allele was more prevalent in the alcoholic patients than in the healthy controls in a study consists of 248 alcohol...
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[GWAS:Alcohol dependence]
among alcoholics, likely to be heavier drinkers
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rs1042173 is a SNP in the solute carrier family 6 (neurotransmitter transporter, serotonin), member 4 SLC6A4 gene. A study of 275 patients seeking treatment for alcoholism concluded that Caucasians of with the rs1042173(T;T) genotype consumed an average of 11.17 drinks per drinking day, compared with an average of 8.58 for carriers of a rs1042173(G) allele (p = 0.0034). While this held true for both men and women, this association was not seen in Hispanics.
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[GWAS:Alcohol dependence]
Frequency: 35.4%
References:1
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Frequency: 43.4%
References:2
References:2
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[GWAS:Alcohol dependence]
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[GWAS:Alcohol dependence]
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rs1693482, also known as Arg272Gln, is a SNP in the alcohol dehydrogenase 1C ADH1C gene. The rs1693482(C) allele is the more common, encoding the amino acid arginine (Arg); the rarer rs1693482(T) allele encodes the variant glutamine (Gln). A study of 575 Irish alcoholics observed an association between rs1693482 and risk for alcohol dependence. On it's own, this SNP is also said to explain 8.4% of the variability in the rate at which alcohol is metabolized, based on a study of 250 Spaniards. More significantly (in a statistical sense), this study concluded that combinations of this SNP and others were shown to affect alcohol metabolism; most of these combinations are represented by the gs211 genoset. Note that the effects of alcohol are higher in individuals who break down (basically, deto...
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[GWAS:None]
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[GWAS:Alcohol dependence]
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[GWAS:Alcohol dependence]
normal; increased agreeableness (?)
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rs1800759 is a SNP in the promoter (regulatory region) of the alcohol dehydrogenase 4 (ADH4) gene. In a study of 500+ patients with either alcohol dependence or drug dependence, rs1800759 was the most significant ADH4 SNP to be associated (in a recessive manner) with increased risk for either condition, at least in Caucasians. In another study, a five-factor model of personality in 243 subjects with substance dependence (175 European Americans [EAs] and 68 African Americans [AAs]), along with 296 healthy control subjects (256 EAs and 40 AAs), was conducted in association with an ADH4 SNP survey. rs1800759(A) alleles and (A;A) genotypes A/A were significantly associated with agreeableness scores.
slightly less drug dependence, decreased effectiveness of analgesics
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Genome-wide association study identifies a potent locus associated with human opioid sensitivity rs2952768(C) was associated with more analgesic requirements ... exhibited less vulnerability to severe methamphetamine or alcohol dependence, fewer eating disorders, and a lower ‘Reward Dependence’ score on a personality questionnaire. The (C;C) genotype was significantly associated with the elevated expression of a neighboring gene, CREB. SNPs in this locus are the most potent genetic factors associated with human opioid sensitivity known to date, affecting both the efficacy of opioid analgesics and liability to severe substance dependence. Our findings provide valuable information for the personalized treatment of pain and drug dependence. [GWAS:Opioid sensitivity]
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[GWAS:Alcohol dependence]
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Alcohol abuse failed to replicate in A genome-wide association study of alcohol dependence. [GWAS:Alcohol dependence]
Frequency: 73.8%
References:1
References:1
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[GWAS:Alcohol dependence]
References:1
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[GWAS:Alcohol dependence]
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This SNP in the GABRA2 gene has been linked to Alcoholism. The strongest association for this SNP is seen when it is a member of a haplotype consisting of the rs279871(A) + rs279845(T) + rs279836(A) alleles . [OMIM:GAMMA-AMINOBUTYRIC ACID RECEPTOR, ALPHA-2; GABRA2]
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This SNP in the GABRA2 gene has been linked to Alcoholism. The strongest association for this SNP is seen when it is a member of a haplotype consisting of the rs279871(A) + rs279845(T) + rs279836(A) alleles . Uncovering genes for cognitive (dys)function and predisposition for alcoholism spectrum disorders: a review of human brain oscillations as effective endophenotypes. The role of GABRA2 in alcohol dependence, smoking, and illicit drug use in an Australian population sample. Role of GABRA2 in trajectories of externalizing behavior across development and evidence of moderation by parental monitoring. Cocaine effects on mouse incentive-learning and human addiction are linked to alpha2 subunit-containing GABAA receptors. [OMIM:GAMMA-AMINOBUTYRIC ACID RECEPTOR, ALPHA-2; GABRA2]
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This SNP in the GABRA2 gene has been linked to Alcoholism. The strongest association for this SNP is seen when it is a member of a haplotype consisting of the rs279871(A) + rs279845(T) + rs279836(A) alleles . [OMIM:GAMMA-AMINOBUTYRIC ACID RECEPTOR, ALPHA-2; GABRA2]
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In 2009, a large, multi-sample replication study failed to find any significant association with Intelligence for this or other SNPs in CHRM2 . Earlier work had observed that this snp (and perhaps its neighbors) influenced intelligence and alcohol dependence CHRM2 gene predisposes to alcohol dependence, drug dependence and affective disorders: results from an extended case-control structured association study. And the earlier and or this pdf poster show association between the CHRM2 gene and intelligence . In this study of ~300 Caucasians, the (T;T) genotype appeared to typically have a 4 point higher IQ than the (A;T) genotype, which had a 4 point higher IQ (on average) than the (A;A) genotype. A nearby SNP, rs324640, showed similar results to rs324650, and was in linkage disequilibrium (...
normal
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[rs27048, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27072. Variations in the DAT1 gene may affect the inattentive subtype of ADHD.
normal
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rs324420 is a SNP, also known as Pro129Thr, in the fatty acid amide hydrolase FAAH gene, which has shown associations with some substance use disorders. rs324420(C) encodes the more common Pro, while the (A) allele encodes the Thr. Among 80 individuals with drug abuse or alcoholism and over 1,000 controls, the odds ratio for risk of problem drug or alcohol use among rs324420(A;A) individuals was 4.5 (CI: 2.2 - 8.4); the odds ratio for risk of street drug use was 2.2 (CI: 1.3–3.7); and the odds ratio for risk of combined street drug use and problem drug/alcohol use was 4.9 (CI: 2.5–9.7) When this study was pooled with the results of another study of 249 subjects with documented multiple different drug addictions compared to drug free individuals of the same ethnic backgrounds, t...
normal
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The rs1799971(G) allele in exon 1 of the mu opioid receptor OPRM1 gene causes the normal amino acid at residue 40, asparagine (Asn), to be replaced by aspartic acid (Asp). In the literature this SNP is also known as A118G, N40D, or Asn40Asp. Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. However, subsequent research results are mixed, and there are other studies both agreeing or disagreeing with this finding Among 200+ alcoholics treated with naltrexone, rs1799971(G) carriers receiving the drug (even without behavioral intervention) had an increased percentage of days abstinent (p = .07) and a decreased percentage of heavy drinking days (...
Magnitude: 0
Frequency: 72.3%
Repute:Good
References:0
Frequency: 72.3%
Repute:Good
References:0
common in complete genomics
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rs13297480(G) a specific high-risk haplotype (p = 0.006, maximum statistic p = 0.051) for alcoholism
normal
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http://www.scientificblogging.com/news_releases/comorbidity_ghrelin_hunger_hormone_implicated_in_alcohol_dependence Jörgen Engel, professor of pharmacology at the Sahlgrenska Academy, University of Gothenburg For this research, scientists recruited 417 Spanish individuals from the general population (n=279) as well as heavy drinkers (n=138) admitted to a hospital for treatment. The study sample – comprised of abstainers, moderate and heavy alcohol drinkers – was then examined for single nucleotide polymorphisms (SNPs) in the pro-ghrelin and growth hormone secretagogue receptors (GHS-R1A) (GHSR) gene. Findings showed that SNP rs2232165 of the GHS-R1A gene was associated with heavy alcohol consumption (and therefore presumably alcohol dependence). SNP rs2948694 of the same g...
normal
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http://www.scientificblogging.com/news_releases/comorbidity_ghrelin_hunger_hormone_implicated_in_alcohol_dependence Jörgen Engel, professor of pharmacology at the Sahlgrenska Academy, University of Gothenburg For this research, scientists recruited 417 Spanish individuals from the general population (n=279) as well as heavy drinkers (n=138) admitted to a hospital for treatment. The study sample – comprised of abstainers, moderate and heavy alcohol drinkers – was then examined for single nucleotide polymorphisms (SNPs) in the pro-ghrelin and growth hormone secretagogue receptors (GHS-R1A) (GHSR) gene. Findings showed that SNP rs2232165 of the GHS-R1A gene was associated with heavy alcohol consumption (and therefore presumably alcohol dependence). SNP rs2948694 of the same g...
common one paper reports increased risk of alcoholism for African-Americans with this genotype.
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This paper found significant association with rs2066702, the SNP that defines ADH1B*3, in African American families. Association was strongest with the ICD-10 definitions of alcoholism, with P=0.046 for PDTsum and 0.029 for PDTaverage; it was also significant for DSM-IV for PDTaverage (P=0.039). The high-risk allele was the C that encodes ADH1B*1, and the low-risk allele encodes ADH1B*3. A review of the (at times conflicting) findings regarding ADH1B genotypes and maternal and fetal alcohol syndromes is available.In some African American] and Native American populations, the ADH1B*3 allele (Arg369Cys in exon 9) is correlated with protection against alcoholism. [PharmGKB:In-Depth This allele has been found in some African American and Native American populations to be correlated with prote...
34 snps
(hide) Allergies
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[GWAS:Self-reported allergy]
increased risk
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rs977785, a SNP purported to be in the promoter of the LY86 gene, is reported to be associated with mite-sensitive allergies in children, based on a study of 500+ Taiwanese patients. The allele that is underrepresented (and thus protective?) is the minor allele, which in dbSNP orientation is rs1334710(A).
average
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rs1334710, a SNP purported to be in the promoter of the LY86 gene, is reported to be associated with mite-sensitive allergies in children, based on a study of 500+ Taiwanese patients. The allele that is underrepresented (and thus protective?) is the minor allele, which in dbSNP orientation is rs1334710(G).
Frequency: 69.9%
References:3
References:3
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Allergies
Magnitude: 0
Frequency: 40.7%
References:16
Frequency: 40.7%
References:16
normal
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rs17388568 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.26 (CI 1.11-1.42), and for homozygotes, 1.58 (CI 1.27-1.95). In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.11 (CI 1.05–1.18). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,963 cases, 2,938 controls; Replication Sample Size: (see Todd 2007); Risk Allele: rs17388568-A). This variant is associated with type 1 diabetes.] [OMIM:DIABETES MELLITUS, INSULIN-DEPENDENT; IDDM] [GWAS:None] [GWAS:...
5 snps
(hide) Allograft rejection
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
normal
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rs4986790, a SNP also known as Asp299Gly (and also 896A/G) in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in th...
normal
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rs4986791, a SNP also known as Thr399Ile (and also 1196C/T) in the TLR4 gene, is often studied along with a cosegregating SNP known as Asp299Gly, rs4986790. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986791 is (T). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in t...
3 snps
(hide) Alopecia Areata
Frequency: 5.3%
References:1
References:1
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[GWAS:Alopecia areata]
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[GWAS:Alopecia areata]
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[GWAS:Alopecia areata]
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[PharmGKB:Non-Curated GWAS Results: A novel susceptibility locus for type 1 diabetes on Chr12q13 identified by a genome-wide association study (Initial Sample Size: 563 cases, 1,146 controls, 483 trios; Replication Sample Size: 549 families, 1092 individuals from 364 trios; Risk Allele: rs1701704-C).] [GWAS:Alopecia areata] [GWAS:Type 1 diabetes]
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[GWAS:None]
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[OMIM:?] [GWAS:Alopecia areata]
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rs3118470 increases susceptibility to Type I Diabetes 1.28 times for carriers of the C allele Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1). Joint genetic susceptibility to type 1 diabetes and autoimmune thyroiditis: from epidemiology to mechanisms. Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes. Genetic association between the interleukin-2 receptor-alpha gene and mode of onset of type 1 diabetes in the Japanese population. Overview of the Rapid Response data. Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families. [GWAS:Alopecia areata]
normal
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This SNP, along with SNPs rs660895 and rs3817964, is a tag SNP for the HLA-DRB1*0401 allele. The HLA-DRB1*0401 allele has been associated with higher risk for rheumatoid arthritis, and in particular, rheumatoid vasculitis. The association is seen particularly for individuals carrying two copies of, i.e. homozygous for, the allele. The reported odds ratio for rs6910071(G;G) homozygotes is 6.2 (CI: 1.01 - 37.9). The risk for rheumatoid arthritis may be higher for individuals carrying one copy (one 'dose') of the HLA-DRB1*0401 allele, if they also carry a different HLA-DRB1 risk allele. In particular, *0401/*0404 individuals are reported to have an odds ratio for rheumatoid vasculitis of 4.1 (CI: 1.1 - 16.2), and *0401/*0101 individuals have an odds ratio of 4.0 (CI: 1.4 - 11.6). rs6910071 wa...
normal
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rs1143634, also known as +3954, is a SNP in the IL-1 beta IL1B gene. A study of 556 adults in the Western Australian coronary heart disease (CHD) population concluded that rs1143634(T;T) homozygotes had larger waist circumference, by 1.8cm on average, compared to major allele (C;C) homozygotes. This association was even more pronounced in patients with higher levels of obesity or inflammatory markers. rs1143634 increases susceptibility to Alopecia Areata 2.67 times for heterozygotes (CT) and 1.13 times for homozygotes (TT) rs1143634 increases susceptibility to Alzheimer's disease 2.33 times for homozygotes (TT) rs1143634 increases susceptibility to Cervical lesions, low-grade squamous intraepithelial lesions 4.29 times for heterozygotes (CT) and 3.57 times for homozygotes (TT) rs1143634 in...
10 snps
(hide) Alpha-1 antitrypsin deficiency
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
common in complete genomics
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rs28929474, also known as Glu342Lys as well as E366K, is a SNP in the serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 SERPINA1 gene. This SNP is the one most frequently leading, when homozygous, to the complications of alpha-1 antitrypsin deficiency and the associated high risk of emphysema and liver disease. Between 1 - 2% of US Caucasians are thought to be (heterozygous) carriers for this SNP, leading some associations, like the Alpha-1 Foundation, to call for mass carrier screening. * 23andMe blog rs28929474(T) increases odds of liver disease in cystic fibrosis patients by 4.17 times. (T;T) at both copies of this SNP causes alpha-1 antitrypsin deficiency; note use of opposite strand nomenclature by this company. Genetic polymorphisms and susceptibilit...
common in complete genomics
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rs17580, also known as the S or PiS allele, is a SNP in the SERPINA1 gene. Levels of alpha-1 antitrypsin (encoded by the SERPINA1 gene) may be reduced in carriers of the rs17580(T) allele, but there is no known association with liver disease or cystic fibrosis. The rs17580 PiS variant is most associated with risk of developing COPD, especially in smokers, but it's association with emphysema is variable. See rs28929474 for the most common pathologic SNP (PiZ) in the SERPINA1 gene. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is T, but test results may be in the plus orientation where the risk allele is A (although currently 23andMe reports the risk allele as T). This SNP has an ambiguous flip which can make...
2 snps
(hide) Alzheimer's disease
APOE E2/E2
2 copies of the APOE2 allele in the APOE gene. The lowest risk of Alzheimer's disease.
Faster aging. Increased risk for Dementia. Less good cholesterol. This reduces HDL ('good') cholesterol. HDL cholesterol removes cholesterol from artery walls and improves health. This SNP seems to be associated with higher blood pressure, less longevity, and more diseases of aging, in particular memory decline and dementia, and lower odds of living to 100, especially in Ashkenazi Jews. Attempting to raise HDL cholesterol may (or may not) be useful to mitigate the effects of this SNP.
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This SNP rs5882 in the CETP gene referred to as ILE405VAL and RSAI405V has been related to ageing and exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated...
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
lower levels of ApoE
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Significant Alzheimer's disease associations with were found for rs449647(A;A) and rs405509(G;G) genotypes (positive), and rs449647(A;T) and rs405509(T;T)
Magnitude: 1.5
Frequency: 10.6%
Repute:Good
References:32
Frequency: 10.6%
Repute:Good
References:32
0.84x decreased risk for Alzheimer's disease
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rs11136000 is a SNP associated with the clusterin CLU gene, which has also been known as the APOJ gene. A study of over 5,000 Alzheimer's disease patients (and over 10,000 controls) found a slight protective effect of the (T) allele of this SNP. rs11136000(T) carriers had a slightly decreased risk for Alzheimer's disease, with an odds ratio of 0.84 (CI: 0.8-0.9, p=1.4x10e-9). The association of this SNP and late-onset Alzheimer's disease was replicated over a total of another 1829 cases (and 2576 controls). A MRI study of ~400 young (average age: 23) healthy carriers of rs11136000(C) alleles found a distinct profile of lower white matter integrity in these individuals that may increase their vulnerability to developing Alzheimer's later in life. To put it another way, 50 years before the a...
0.85x decreased risk for Alzheimer's disease
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rs3851179 is a SNP upstream of the PICALM gene. A study of over 5,000 Alzheimer's disease patients (and over 10,000 controls) found a slight protective effect of the (A) allele of this SNP. rs3851179(A) carriers had a slightly decreased risk for Alzheimer's disease, with an odds ratio of 0.85 (CI: 0.8-0.9, p=1.9x10e-8). The association of this SNP and late-onset Alzheimer's disease was replicated over a total of another 1829 cases (and 2576 controls). [GWAS:Alzheimer's disease]
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Alzheimer's disease associated, based on large 2011 study Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. The prevalence of CD33 and MS4A6A variant in Chinese Han population with Alzheimer's disease. [GWAS:None]
slightly higher risk for Alzheimers in Caucasians but not Asians This variant has been reported to be associated with a slightly higher risk for Alzheimers disease in Caucasians but not in Asians.
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rs1064039, also known as G73A, Ala25Thr or A25T, is a variant in the cystatin C CST3 gene. A relatively small study (167 patients) concluded that rs1064039(A;A) genotypes had about a 3 fold increase in risk for exudative age-related macular degeneration (ARMD). A meta-analysis of 2,410 cases and 2,539 controls reported that although the rs1064039(A) allele is associated with about a 1.5x increased odds ratio for developing Alzheimer's disease in Caucasians, no increased risk was seen in Asians. [OMIM:?]
complex! see rs4880
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The rs4880(T) allele, part of the codon for amino acid valine at codon 16 of the antioxidant protein from the mitochrondrial superoxide dismutase 2 SOD2 gene, is the most common in most populations studied. The rs4880(C) allele gives rise to an alanine at this position is it also known as Val16Ala manganese superoxide dismutase, or A16V. There appears to be some conflict in the literature over the effect of this SNP. Having a valine at codon 16 is said to reduce enzyme activity , and thus lead to increased oxidative stress, yet in at least one study of the actual enzyme levels measured in people, SOD2 activity was 33% higher in (C;T) or (T;T) individuals compared to (C;C) individuals . Regardless of how this resolves, several phenotypic associations have been reported for this SNP, includi...
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rs2160525 is in linkage disequilibrium with a polymorphism that increases susceptibility to late-onset Alzheimer's disease (LOAD) 1.30 times for carriers of the G allele.
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Alzheimer's disease associated, based on large 2011 study
in ALZ patients, increased risk of delusions
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A significant association between delusions and the rs6494223(T) allele (odds ratio 1.63, CI: 1.22-2.17, p = 0.014, ) was found in a cohort of Alzheimer's disease patients in Northern Ireland.
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The risk allele is T (in dbSNP orientation), according to a table published by the National Human Genome Research Institute. [GWAS:Alzheimer's disease]
normal
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Conflicting reports of possible small increase in Alzheimer's risk. Currently dubious at best. rs2373115 is one of several SNPs in the GAB2 gene indicating an increased risk (OR 4.1) of late-onset Alzheimer's disease, but apparently only in individuals also carrying ApoE4 alleles, i.e. rs429358(C) alleles rs2373115 marker does not modify the risk of Alzheimer's disease in Spanish APOE e4 carriers. rs2373115(G) is the risk allele. (p = 9 x 10(-11)) was associated with an odds ratio of 4.06 (confidence interval 2.81-14.69) However, a separate study of 1,749 Alzheimer patients concluded that this GAB2 SNP is 'at best a minor genetic determinant' since the authors of this study observed only a slight tendency for an increase of the (G;G) genotype (odds ratio of 1.3 vs (G;T) and (T;T), CI:1.0-1...
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Linked to increased risk of Alzheimer's disease. [GWAS:Alzheimer's disease biomarkers]
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Late-onset Alzheimer's disease (rs201825, p-value = 6.1 x 10-7 )
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This SNP is near the gene for lecithin retinol acyltransferase (phosphatidylcholine-retinol O-acetyltransferase) or LRAT, which is involved in Vitamin A metabolism; the risk allele is reportedly G (in dbSNP orientation). [PharmGKB:Non-Curated A genome-wide association study for late-onset Alzheimer's disease using DNA pooling. (Initial Sample Size: 1,082 cases, 1,239 controls; Replication Sample Size: 1,400 additional controls); (Region: 22q13.33; Reported Gene: CPT1B; Risk Allele: rs727153-C) This variant is associated with Alzheimer's disease.] [GWAS:Alzheimer's disease]
Frequency: 25.9%
References:1
References:1
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rs11609582 increases susceptibility to Alzheimer's disease 1.78 times for heterozygotes (AT) and 1.86 times for homozygotes (TT)
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genomeweb rs4420638 rs11159647 and rs3826656 were also significantly associated with Alzheimer's disease [PharmGKB:Curated GWAS results: Genome-wide Association Analysis Reveals Putative Alzheimer's Disease Susceptibility Loci in Addition to APOE. (Initial Sample Size: 941 affected individuals, 404 unaffected individuals; Replication Sample Size: 1,767 affected individuals, 838 unaffected individuals); (Region: 19q13.33; Reported Gene(s): CD33; Risk Allele: rs3826656-?); (p-value= 0.000006).This variant is associated with Alzheimer's disease.] [GWAS:Alzheimer's disease]
Frequency: 28.6%
References:2
References:2
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rs10883421 is one of 2 SNPs in the DNMBP gene that has been associated with increased risk for late-onset Alzheimer's disease in both Japanese and Belgian populations; the other SNP being rs3740057. [PharmGKB:Curated This variant is associated with Alzheimer dementia in the Belgian population]
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The risk allele associated with late-onset Alzheimer's disease is A. [PharmGKB:Non-Curated GWAS results: A genome-wide association study for late-onset Alzheimer's disease using DNA pooling. (Initial Sample Size: 1,082 cases, 1,239 controls; Replication Sample Size: 1,400 additional controls); (Region: 19q13.32; Reported Gene(s): PVRL2, TOMM40, APOE; Risk Allele: rs6859-A); (p-value= 5.99999999999999E-14).This variant is associated with Alzheimer's disease.] [GWAS:Alzheimer's disease]
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[GWAS:Alzheimer's Disease]
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a significant association between rs3924999 and Alzheimer's disease with psychosis [OMIM:NEUREGULIN 1; NRG1]
Frequency: 33.3%
References:6
References:6
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genomeweb rs4420638 rs11159647 and rs3826656 were also significantly associated with Alzheimer's disease [PharmGKB:Curated GWAS results: Genome-wide Association Analysis Reveals Putative Alzheimer's Disease Susceptibility Loci in Addition to APOE. (Initial Sample Size: 941 affected individuals, 404 unaffected individuals; Replication Sample Size: 1,767 affected individuals, 838 unaffected individuals); (Region: 14q31.2; Reported Gene(s): Intergenic; Risk Allele: rs11159647-?); (p-value= 0.000002).This variant is associated with Alzheimer's disease.] [GWAS:Alzheimer's disease]
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rs2227564 A functional polymorphism within plasminogen activator urokinase (PLAU) is associated with Alzheimer's disease . *rs2227564 distribution of four tagSNPs (rs2227562 in intron 5, rs2227564 in exon 6, rs2227571 in intron 9, and rs4065 in 3' UTR) in the PLAU gene in a large case-control study of Alzheimer's disease No association of a non-synonymous PLAU polymorphism with Alzheimer's disease and disease-related traits. Elevated amyloid beta protein (Abeta42) and late onset Alzheimer's disease are associated with single nucleotide polymorphisms in the urokinase-type plasminogen activator gene. Linkage disequilibrium patterns and tagSNP transferability among European populations. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disea...
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[GWAS:Alzheimer's Disease]
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[PharmGKB:Non-Curated GWAS results: Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease. (Initial Sample Size: 844 cases, 1,255 controls; Replication Sample Size: 1,547 cases, 1,209 controls); (Region: Xq21.31; Reported Gene(s): PCDH11X; Risk Allele: rs2573905-?); (p-value= 0.0000002).This variant is associated with Alzheimer's disease.] [GWAS:Alzheimer's disease]
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Alzheimer's disease associated, based on large 2011 study [GWAS:Alzheimer's disease (late onset)]
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Alzheimer's disease rs3824968 Association between genetic variants in sortilin-related receptor 1 (SORL1) and Alzheimer's disease in adults with Down syndrome. No association of SORL1 SNPs with Alzheimer's disease. The neuronal sortilin-related receptor gene SORL1 and late-onset Alzheimer's disease. Assessment of Alzheimer's disease case-control associations using family-based methods. Allelic mRNA expression of sortilin-1 (SORL1) mRNA in Alzheimer's autopsy brain tissues. Association of distinct variants in SORL1 with cerebrovascular and neurodegenerative changes related to Alzheimer disease. Endophenotypes in normal brain morphology and Alzheimer's disease: a review. Association of SORL1 gene variants with Alzheimer's disease. Use of genetic variation as biomarkers for Alzheimer's diseas...
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SNP rs8702, located in the KLC1 gene, has been reported to have a protective effect against the occurrence of multiple sclerosis. Specifically, the odds of a rs8702(G;G) individual - as oriented to the dbSNP entry, not as published - are reported to be 0.21 (CI: 0.018 - 0.88). A study of ~800 Swedish patients with Alzheimer's disease did not find an association to rs8702 independently, however, rs8702 interacted with ApoE4 carrier status in AD (p=0.006). Variability in the kinesin light chain 1 gene may influence risk of age-related cataract. Gene-environmental effects behind leukoaraiosis: a silent genetic variant of the kinesin protein can be activated in a subject with poorly controlled long-lasting hypertension.
normal
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A case-control study of 300 patients with Alzheimer's disease found that subjects carrying both the rs2071746(T;T) and rs242557(A;A) genotypes had a 6.65x increased risk (CI: 1.12-39.29; p = 0.037) compared to subjects without these risk genotypes. This combination of SNPs is encapsulated in the gs124 genoset.
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Polymorphism of rs1044925 in the acyl-CoA:cholesterol acyltransferase-1 gene and serum lipid levels in the Guangxi Bai Ku Yao and Han populations. C allele associated with lower serum lipids in a specific ethnic group. Genetic association of acyl-coenzyme A: cholesterol acyltransferase with cerebrospinal fluid cholesterol levels, brain amyloid load, and risk for Alzheimer's disease. A allele associated with lower risk of Alzheimer's disease.
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[GWAS:Alzheimer's disease]
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Alzheimer's disease associated, based on large 2011 study Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Genome-wide association of familial late-onset Alzheimer's disease replicates BIN1 and CLU and nominates CUGBP2 in interaction with APOE. Meta-analysis for genome-wide association study identifies multiple variants at the BIN1 locus associated with late-onset Alzheimer's disease. [GWAS:None]
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linked to Alzheimer's disease
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The G allele of this SNP in the TOMM40 gene may be associated with late-onset Alzheimer's disease. Association of ApoE genetic variants with obstructive sleep apnea in children. Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. A genome-wide association study for late-onset Alzheimer's disease using DNA pooling. Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease. Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Genome-wid...
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The C allele of this SNP may be associated with rate of progression of Alzheimer's disease, according to an article in PLoS Genetics. It does not appear to affect risk or age of onset.
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Alzheimer's disease associated, based on large 2011 study
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rs4877365 has been linked to Alzheimer's disease
Normal
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rs6733839 and rs744373 are less than 2,000 base pairs apart,and they have similar ORs and MAFs. Therefore, it seems reasonable to suspect that these 2 SNPs are actually reporting the same signal. [GWAS:None]
Frequency: 50.0%
References:1
References:1
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[GWAS:Alzheimer's disease]
None
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rs4934 increases susceptibility to Alzheimer's disease 2.56 times for (A;A) homozygotes systolic blood pressure increased with rs4934(A) finds no association between rs4934 and pulmonary emphysema Algorithm for automatic genotype calling of single nucleotide polymorphisms using the full course of TaqMan real-time data. The genetics of chronic obstructive pulmonary disease. Lung cancer susceptibility model based on age, family history and genetic variants.
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SNP rs2070045, a variant of the SORL1 gene, has been reported to be associated with Alzheimer's disease. However, a subsequent study of over 2,000 patients found a weak (at best) association.
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linked to rs4938933 and Alzheimer's disease
Frequency: 58.4%
References:11
References:11
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Alzheimer's disease risk for non ApoE4 carriers is affected by the heterozygous form of rs6265, as well as the diplotypes of rs6265, rs11030104, and rs2049045. [GWAS:Body mass index]
no positive effect of AChE inhibitors for Alzheimer's patients
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rs733722, also known as -5293C>T, is a SNP near the choline acetyltransferase CHAT gene. A study of 121 Alzheimer's disease patients treated primarily with the acetylcholinesterase (AChE) inhibitors donepezil or galantamine found different rates of mental decline depending on rs733722 genotypes. Individuals of rs733722(C;C) genotype effectively showed declines in cognition over time equivalent to untreated patients, whereas rs733722(C;T) individuals showed less decline, and rs733722(T;T) patients had a negligible decline over the course of the study (~15 months). An earlier study by these authors found no association between SNPs in this gene and actual risk for Alzheimer's.
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[GWAS:Alzheimer's Disease]
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[GWAS:Alzheimer's Disease]
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rs2297404, rs2230808, and rs2020927 haplotype (CAC) was more prevalent in the Alzheimer's disease group (0.323 in AD vs. 0.202 in control); while haplotype1 (TGG) was over-represented in the healthy controls (0.595 in control vs. 0.493 in AD) ABCA1 modulates CSF cholesterol levels and influences the age at onset of Alzheimer's disease. ABCA1 polymorphisms and Alzheimer's disease. Apolipoprotein E levels in cerebrospinal fluid and the effects of ABCA1 polymorphisms. The effect of ABCA1 gene polymorphisms on ischaemic stroke risk and relationship with lipid profile. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. A survey of ABCA1 sequence variation confirms association with dementia. A polymorphism of the ABCA1 gene confers sus...
Frequency: 63.1%
References:3
References:3
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Alzheimer's disease associated, based on large 2011 study
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[GWAS:Alzheimer's disease]
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[GWAS:Alzheimer's disease]
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[PharmGKB:Curated GWAS results: Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease. (Initial Sample Size: 492 cases, 496 controls; Replication Sample Size: 238 cases, 220 controls); (Region: 19q13.31; Reported Gene(s): ZNF224; Risk Allele: rs2061333-?); (p-value= 0.000002).This variant is associated with Alzheimer's disease.] [GWAS:Alzheimer's disease]
Frequency: 72.6%
References:1
References:1
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[GWAS:Alzheimer's disease]
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rs2297404, rs2230808, and rs2020927 haplotype (CAC) was more prevalent in the Alzheimer's disease group (0.323 in AD vs. 0.202 in control); while haplotype1 (TGG) was over-represented in the healthy controls (0.595 in control vs. 0.493 in AD) Effect of ABCA1 variant on atherogenic dyslipidaemia in patients with Type 2 diabetes treated with rosiglitazone.
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Linked to increased risk of Alzheimer's disease. [GWAS:Alzheimer's disease biomarkers]
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In a study of 1,757 cases of Alzheimer's disease and 6,295 controls, an interaction was replicated between IL6 genotype rs2069837(A;A) and IL10 genotype rs1800871(C;C). The synergy factor (SF) was 1.63 (CI: 1.10-2.41, p = 0.01), controlling for age, gender and ApoE4 genotype.
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Having one or more copies of a C at rs2248663 in people without ApoE-ε4 was linked to lower age of Alzheimer's disease onset and more plaques. 23andMe blog
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rs145518263 Alzheimer's disease assocation
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rs61751103 Alzheimer's disease assocation
1.5x increased risk for Alzheimer's disease
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A case-control study of 471 Italian late-onset Alzheimer's disease patients aged 60 years or older, and 254 subjects with no neurodegenerative disorders serving as the control group, found that the rs2177369(G;G) genotype (in dbSNP orientation) a risk factor with an odds ratio of 1.56 (CI: 1.10-2.22, p = 0.01). Refreshingly, the authors call their results 'far from definitive'.
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associated Alzheimer's disease especially in women, increasing the risk of low cognitive performance and dementia low cognitive performance and dementia in the elderly, elevated levels of S100beta2 mRNA in AD brains, especially in women
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rs2758346 rs4880 and rs2855116 association with Alzheimer's disease The T allele appears to be more common in late-onset Alzheimer's disease.
normal
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rs3025786 is a SNP in the presenilin 1 PSEN1 gene. A study of a Spanish case-control sample of 1,183 individuals showed rs3025786 was associated with Alzheimer's disease in an ApoE-specific manner: more specifically rs3025786(C) allele carriers have a decreased AD risk among carriers of the ApoE4 allele.
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rs3758505, rs4646953 and rs4646954 influence Alzheimer's disease [OMIM:INSULIN-DEGRADING ENZYME; IDE]
normal
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rs5963409 is a SNP in the ornithine carbamoyltransferase OTC gene; this SNP is also known as the -389 G/A SNP. Previous association studies were extended to a population of 2113 Alzheimer's disease cases and 1580 controls from northern France, western France, the United Kingdom and Italy. The rs5963409(A) minor allele was weakly but significantly associated with an increased risk of developing Alzheimer's disease (odds ratio 1.19, p = 0.004). This association was independent of age and ApoE status.
References:1
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rs63750812, also known as V148I or Val148Ile, is a SNP in the presenilin PSEN2 gene. Inherited as an autosomal dominant, the rare rs63750812(A) allele is reported to be causative for early-onset Alzheimer's disease. However, the AlzForum also reports that 'No change in proteolytic products PSEN2-CTF and PSEN2-NTF; no change in Aβ42 levels or the Aβ42/Aβ40 ratio', and in combination with the original report, this allele may be more of a predisposing than causative mutation.
normal
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The ancestral allele is C. The rs7412(T) allele, also known as Arg176Cys, generally indicates the presence of an Apoε2 allele; see the ApoE page for a full discussion of the ApoE alleles and their association with Alzheimer's disease. Another SNP related to ApoE is rs429358. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs7412(C) allele were more likely to gain significant weight compared to rs7412(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs4765623, were also significantly associated with weight profiles in these patients. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity ...
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association of the rs7483 SNP with late-onset Alzheimer's disease
normal
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(G;G) showed a 1.9-fold increased risk of Alzheimer's disease (95 % CI 1.16-3.10, p = 0.003)
no clear risk
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rs2986017, also known as L86P, is a SNP in the CALHM1 gene. This gene encodes a multipass transmembrane glycoprotein that is involved in the control of cytosolic calcium concentrations and cerebral amyloid-β levels. In case-control studies of 3,404 participants, the rs2986017(T) allele was significantly associated with late-onset Alzheimer's disease. The allele-specific odds ratio was 1.44 (CI: 1.27–1.59, p = 2x10e−10). A study of 62 Belgian Alzheimer's disease patients and 519 ethnically matched control individuals found no evidence of association between rs2986017 and risk of disease, nor with onset age. [PharmGKB:Curated This variant increases amyloid-beta levels by interfering with CALHM1-mediated Ca(2+) permeability. The SNP is signific...
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Alzheimer's disease associated, based on large 2011 study
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rs12316150, a SNP also known as +1071, is located in the 3' untranslated region of the oxidized low density lipoprotein (lectin-like) receptor 1 OLR1 gene, which is also known as the LOX-1 gene. The rs12316150 risk allele has been associated with increased risk for Alzheimer's disease in several studies of ~200 Southern Italian Alzheimer patients, but only within the context of a haplotype including one or both of neighboring SNPs rs1050283 and rs669.
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An initial case-control study of 300 patients with Alzheimer's disease found that subjects carrying both the rs2071746(T;T) and rs242557(A;A) genotypes had increased risk, however the confidence interval was huge (CI: 1.12-39.29; p = 0.037) and later studies have either failed to replicate the results or shown them to only partially hold in APOE4 carriers. Reports that they found only 'nominally significant' association between Alzheimer's and rs242557 in ApoE4 positive individuals. [OMIM:?] [GWAS:None]
normal
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rs5984894 is a SNP located within an intron of the protocadherin 11 PCDH11X gene, on the X chromosome. A study of 2,391 patients with late-onset Alzheimer's disease reports that rs5984894 is particularly associated with increased risk for the disease in females, as compared to males. In this study, the patients were Americans of European descent, and 62% were female. Odds ratios were 1.75 (CI: 1.42–2.16) for female homozygotes (p = 2 x 10e-7) and 1.26 (CI: 1.05–1.51) for female heterozygotes (p = 0.01) compared to rs5984894(G;G) females. For male rs5984894(-;A) hemizygotes (p = 0.07, which may mean this is insignificant since it is above the traditional cut-off of 0.05) compared to male rs5984894(-;G) noncarriers, the odds ratio was 1.18 (CI: 0.99–1.41). A more recent and...
normal
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rs726601 is among several SNPs in the SORL1 gene that show some association with increased (or decreased) risk for Alzheimer's disease in a study of 1,400 Caucasians.
normal
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rs1784931 is among several SNPs in the SORL1 gene that show some association with increased (or decreased) risk for Alzheimer's disease in a study of 1,400 Caucasians.
normal risk for Alzheimer's; higher total and LDL cholesterol in females
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RNA made containing the rs688(T) SNP, a variant near exon 12 of the low-density lipoprotein receptor (LDLR) that is a receptor for ApoE proteins, is spliced at lower efficiency in males. Presumably due to this, the rs688(T;T) genotype was associated with increased risk for Alzheimer's disease odds in males (odds ratio 1.49, CI: 1.13-1.97, uncorrected p=0.005), but not in females. The presence of the rs688(T) allele associates with increased total and LDL-cholesterol in female members of the Framingham Offspring Study; rs688 was not associated with significant differences in HDL-cholesterol. The largest rs688-associated cholesterol differences were observed in pre-menopausal women. Taken together, rs688, a SNP present in approximately 60% of Caucasians, is associated with significant 10% in...
normal
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rs3818361 is a SNP associated with the complement component (3b/4b) receptor 1 CR1 gene. The association of this SNP and late-onset Alzheimer's disease was replicated over a total of another 1829 cases (and 2576 controls). The odds ratio for rs3818361(T) allele was 1.15 (note the p value was 0.014). [GWAS:None]
1.18x increased risk for LOAD
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Nominally significant association found for this SNP with late-onset Alzheimer's disease (odds ratio 1.18, p=0.024) in a study of ~1000 Caucasian patients, but it would not have withstood statistical correction for multiple testing.
Normal/Average risk for Alzheimer's
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Apolipoprotein E ApoE status is technically defined by two different SNPs, rs429358 and rs7412. This SNP, rs4420638, is situated about 14kb away in the adjacent ApoC1 gene and is co-inherited with ApoE and thus associated with late-onset Alzheimer's disease. rs4420638 (the proxy SNP) is not independent of rs429358. These two SNPs are correlated with each other and it's believed that most of the association with AD at rs4420638 is due to its proximity to rs429358. That said, rs4420638 is not a perfect proxy for rs429358 either -- rs4420638 correlates better for certain genotypes and for certain ethnicities. For example, if you have the genotype at rs4420638 that is more correlated with the e4 allele of APOE, you still only have a 50% chance of actually having the e4 allele. And rs4420638 is...
common/normal Val/val (normal) variant of the Val66Met snp in the BDNF gene that codes for brain-derived neurotrophic factor. Met/met is associated with susceptibility to neuropsychiatric disorders.
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
0.5x decreased risk for endometriosis
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rs1800871(C) carriers are associated with a reduced endometriosis risk by approximately 2x compared with the common rs1800871(T;T) genotype in a study of 196 Chinese patients. rs2222202 (C/T) (p=0.03) and rs1800871 (C/T) (p=0.05) showed significant allelic associations with pediatric onset Crohn's disease. rs1800871(T) carriers were 3x more likely to have their pregnancies terminate early (<10 weeks) than (C) carriers, based on a study of ~500 pregnancies. In a study of 1,757 cases of Alzheimer's disease and 6,295 controls, an interaction was replicated between IL6 genotype rs2069837(A;A) and IL10 genotype rs1800871(C;C). The synergy factor (SF) was 1.63 (CI: 1.10-2.41, p = 0.01), controlling for age, gender and ApoE4 genotype. 23andMe reports that each G allele at rs1800871 is associat...
normal
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The rs1803274(A) allele encodes a version of the butyrylcholinesterase enzyme known as the K variant; it may also be known as CHE*539T or BCHE*539T. The allele produces a 30% reduction in serum butyrylcholinesterase activity, and it is often co-inherited with the SNP encoding the so-called 'atypical' butyrylcholinesterase, rs1799807. Although not replicated by other studies, some studies have found, at least in certain populations, a possible association between this SNP and risk for Alzheimer's disease (independent of ApoE4 status): * reports ~2x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 135 Canadian patients * reports ~3.5x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 175 patients f...
normal http://www.diygenomics.org/webapp/gen_data.php
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Located close to ApoE4, yet may independently (also) influence risk of Alzheimer's disease. A case-control study of 381 patients found a 2x higher risk for Alzheimer's disease associated with the rarer rs2075650(G) allele. This allele is associated with earlier onset of Alzheimer's disease, by ~7 years. (news) The data from this study are available online at The association of this SNP with late-onset Alzheimer's disease] was confirmed by a study reported in PLoS Genetics. The A allele of this SNP is one of 150 identified as relevant to exceptional longevity in Recent work suggests, however, that the linkage disequilibrium between rs2075650 and the ApoE ε4 defining SNP rs429358 means that there may be little, if any, independent effect of rs2075650 on Alzheimer's risk. rs2075650] was ...
C1 subtype of transferrin; common in clinvar
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rs1049296, also known as Pro570Ser, is best known as the basis for the C1/C2 subtypes of the transferrin TF gene. The rs1049296(C) allele encodes the C1 subtype, and the rarer rs1049296(T) allele encodes the C2 subtype. Involved in the transport of iron, transferrin and its subtypes have been linked at times to various conditions, perhaps most notably Alzheimer's disease. One meta-analyis of 19 studies with 6310 cases and 13661 controls concluded that the C2 allele, rs1049296(T), was associated with slightly increased risk for Alzheimer's, with odds ratios around 1.1-1.2. Pathogens may scavenge iron, and the body's attempts to sequester it from such pathogens are a form of defense termed nutritional immunity. One explanation for the presence of the C2 TF subtype in humans is that it may re...
common in complete genomics
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rs6583817, also known as v311, is a SNP within an intron of the IDE gene, which encodes the insulin-degrading enzyme. Late onset Alzheimer's disease is a neurodegenerative condition in which the brain develops large numbers of extracellular senile plaques composed primarily of aggregated amyloid-B proteins as well as intraneuronal neurofibrillary tangles composed mainly of aggregated tau protein. One notable function of insulin-degrading enzyme is its ability to degrade amyloid-B and therefore to influence the amount of amyloid-B found in the brain. A study of ~3,000 patients (and an equal number of matched controls) found that carriers of one or two minor alleles, i.e. rs6583817(T), had ~2x higher levels of insulin-degrading enzyme (p < 10e-8), lower levels of amyloid-B, and a (slightl...
common in complete genomics
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rs7910977 is a SNP of the IDE gene, which encodes the insulin-degrading enzyme. Late onset Alzheimer's disease is a neurodegenerative condition in which the brain develops large numbers of extracellular senile plaques composed primarily of aggregated amyloid-B proteins as well as intraneuronal neurofibrillary tangles composed mainly of aggregated tau protein. One notable function of insulin-degrading enzyme is its ability to degrade amyloid-B and therefore to influence the amount of amyloid-B found in the brain. The rs7910977(T) allele is associated with reduced risk of Alzheimer's disease in one study of ~3,000 patients, and in this study, the conclusion was that it was most likely due to near perfect linkage with rs6583817, a nearby functional variant. rs6583817(T) allele carriers had an...
Magnitude: 0
Frequency: 78.8%
Repute:Good
References:5
Frequency: 78.8%
Repute:Good
References:5
common on affy axiom data
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news Alzheimer's disease [PharmGKB:Curated GWAS results: Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease. (Initial Sample Size: 492 cases, 496 controls; Replication Sample Size: 238 cases, 220 controls); (Region: 12q13.11; Reported Gene(s): FAM113B; Risk Allele: rs11610206-?); (p-value= 0.0000003).This variant is associated with Alzheimer's disease.] [GWAS:Alzheimer's disease]
normal
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Alzheimer's disease associated, based on large 2011 study 'The minor allele of Rs3764650 in ABCA7 was associated with a later age at onset and shorter disease course' according to http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511432/ [GWAS:None]
normal
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Nominally significant association found for this SNP with late-onset Alzheimer's disease (odds ratio 0.79, p=0.022) in a study of ~1000 Caucasian patients, but it would not have withstood statistical correction for multiple testing.
Magnitude: 0
Frequency: 86.7%
Repute:Good
References:5
Frequency: 86.7%
Repute:Good
References:5
common on affy axiom data
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This SNP in the MTHFD1L gene is associated with late-onset Alzheimer's disease, according to an article in PLoS Genetics. [PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
normal risk
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rs1799724, a SNP near the tumor necrosis factor TNF gene, was found in a study of ~500 Caucasians to be both an independent risk factor for the development of Alzheimer's disease and also a modifier of the risk for individuals carrying ApoE4 alleles. On its own, the rs1799724(T) allele led to an odds ratio of 1.63 (CI: 1.13-2.34, p=0.009). In carriers of ApoE4 alleles, the odds ratio changed from 2.92 (CI: 2.00-4.27) in the absence of rs1799724(T) to an OR of 6.65 (CI: 3.26-13.55, p=0.03) in its presence. In a Chinese study , post-menopausal women were significantly more likely to have low bone mineral density if they had *CC-AA genotypes in rs1799724-rs1800629 * a haplotype of rs1799724-rs1800629-rs6254-rs6256-IL-1ra-rs2227956-rs1801197 news cigarette smoking and gastric cancer risk [Pha...
normal
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rs4986790, a SNP also known as Asp299Gly (and also 896A/G) in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in th...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common/normal
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rs113809142, also known as c.4416+2T>G, is one of several loss-of-function ABCA7 mutations associated with Alzheimer's disease initially in Icelanders, and then replicated in other populations. Carriers of one rare rs113809142(G) allele are at roughly more than twice the risk for developing late-onset Alzheimer's disease compared to people having the most common genotype (T;T); the odds ratio is 4.47, p=3.4 × 10e−7.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs28936379, also known as M239V or Met239Val, is a SNP in the presenilin 2 PSEN2 gene. Inherited as an autosomal dominant, the rare rs28936379(G) allele is considered causative for early-onset Alzheimer's disease. [OMIM:ALZHEIMER DISEASE, FAMILIAL, 4]
common
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This SNP, located in the fourth exon of the ApoE gene, affects the amino acid at position 130 of the resulting protein. The more common rs429358 allele is (T). If the allele is (C) and the same chromosome also harbors the rs7412(C) allele, the combination is known as an APOE-ε4 allele. The APOE-ε4 allele has a strong influence on the risk of Alzheimer's disease. Both deCODEme and 23andMe (v3 chip) test for this SNP. Many studies have estimated the level of risk, and it varies depending on age, sex, ethnicity, and other factors. One meta-analysis estimated the odds ratios for homozygous rs429358(C;C) individuals compared to the more common ApoE3/ApoE3 homozygotes to be 12x for late-onset Alzheimer's and 61x for early-onset disease. Meta-analyses have also supported the association between t...
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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rs63749824, also known as A79V or Ala79Val, is a SNP in the presenilin 1 PSEN1 gene. Inherited as an autosomal dominant, the rare rs63749824(T) allele is considered pathogenic for late-onset Alzheimer's disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs63749851, also known as T122P or Thr122Pro, is a SNP in the presenilin 2 PSEN2 gene. Inherited as an autosomal dominant, the rare rs63749851(C) allele is considered causative for early-onset Alzheimer's disease, as reported in . If you are aware of individuals carrying this allele who are past the age of 50 and who are not Alzheimer patients, please let us know. [OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
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rs63749884, also known as M239I or Met239Ile, is a SNP in the presenilin 2 PSEN2 gene. Inherited as an autosomal dominant, the rare rs63749884(A) allele is considered causative for early-onset Alzheimer's disease; see . However, only three of the five individuals in the family studied who carried this mutation developed Alzheimer's; the other two did not. The penetrance of this mutation is therefore clearly not 100%, for reasons that are unknown. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs63750048, also known as A85V or Ala85Val, is a SNP in the presenilin 2 PSEN2 gene. Inherited as an autosomal dominant, the rare rs63750048(T) allele is reported to lead to an atypical early-onset Alzheimer's disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs63750110, also known as D439A or Asp439Ala, is a SNP in the presenilin 2 PSEN2 gene. Inherited as an autosomal dominant, the rare rs63750110(C) allele is considered causative for early-onset Alzheimer's disease; see . [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs63750197, also known as S130L or Ser130Leu, is a SNP in the presenilin 2 PSEN2 gene. Although based on small numbers of patients, the rare rs63750197(T) allele has been reported to be associated with both early-onset Alzheimer's disease and a form of dilated cardiomyopathy., However, the pathogenicity is considered 'unclear', and the AlzForum summary states, 'No change in proteolytic products PSEN2-CTF and PSEN2-NTF; no change in Aβ42 levels or the Aβ42/Aβ40 ratio.' [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs63750526, also known as A246E or Ala246Glu, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63750526(A) allele is reported as causative for early-onset Alzheimer's disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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rs63750577, also known as S170F or Ser170Phe, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63750577(T) allele is considered causative for early-onset Alzheimer's disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs63750590, also known as H163R or His163Arg, is a SNP in the presenilin 1 PSEN1 gene. Based on limited data, the rare rs63750590(G) allele is considered causative for early-onset Alzheimer's disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs63750599, also known as L85P or Leu85Pro, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63750599(C) allele is considered causative for early-onset Alzheimer's disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs63750666, also known as T430M or Thr430Met, is a SNP in the presenilin 2 PSEN2 gene. Acting as an autosomal dominant, the rare rs63750666(T) allele has been suggested to lead to early-onset Alzheimer's disease. However, a sibling who shared this mutation with an Alzheimer's patient did not show signs of early-onset disease, so this mutation may have reduced penetrance. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs63750815, also known as V89L or Val89Leu, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63750815(T) allele is considered causative for early-onset Alzheimer's disease.
Magnitude: 0
Repute:Bad
References:1
Repute:Bad
References:1
normal
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In APP source Detected in 1 patient with 2 ischemic strokes and myocardial infarction. No family history; no amyloid deposition. The variant also makes developing Alzheimer's disease four times less likely across all age groups. 'It confers extraordinarily strong protection,' said Stefansson. source http://www.decodeyou.com/decode-genetics-discovers-mutation-conferring-protection-against-alzheimers-disease-and-cognitive-decline-in-elderly/ http://blog.personalgenomes.org/2012/08/01/the-predominant-variant-of-the-app-gene-greatly-increases-risk-for-alzheimers-disease-and-cognitive-decline/
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs63750900, also known as R269H or Arg269His, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63750900(A) allele is considered causative for early-onset Alzheimer's disease.
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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rs63751037, also known as M139V or Met139Val, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63751037(G) allele is considered causative for early-onset Alzheimer's disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs63751144, also known as L174M or Leu174Met, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63751144(A) allele is considered causative for early-onset Alzheimer's disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs63751163, also known as L250S or Leu250Ser, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63751163(C) allele is considered causative for early-onset Alzheimer's disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs63751229, also known as P267S or Pro267Ser, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63751229(T) allele is considered causative for early-onset Alzheimer's disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs63751320, also known as Y256S or Tyr256Ser, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63751320(C) allele is considered causative for early-onset Alzheimer's disease.
Magnitude: 0
Repute:Good
References:15
Repute:Good
References:15
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rs75932628(T), a SNP in the TREM2 gene on chromosome 6 resulting in an R47H substitution, was found to confer a significantly higher risk of Alzheimer's disease based on two articles published together in the New Engl. J. of Med. In one study, the odds ratio for rs75932628(T) was 2.9 (CI: 2.09 to 4.09, P=3.42×10−10). The mutation had a frequency of 0.46% in controls 85 years of age or older. The authors also observed the association in additional sample sets (odds ratio, 2.90; 95% CI, 2.16 to 3.91; P=2.1×10−12 in combined discovery and replication samples), and found that carriers of rs75932628-T between the ages of 80 and 100 years without Alzheimer's disease had poorer cognitive function than noncarriers (P=0.003). In the other study, analysis of the rs75932628(T) i...
normal
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This SNP, a synonymous substitution in the ABCA2 gene, has been linked to early onset Alzheimer's disease with an odds ratio of 3.8 for disease development in carriers of the A allele (in dbSNP orientation) compared to controls (95% CI 2-7.3), based on a study of ~400 Caucasian patients. Subsequently, this association was replicated in a Western European population (n=291, p=0.008), but not in a second sample from Southern Europe. rs908832 was not polymorphic in a Japanese sample. Furthermore, rs908832 was not associated with either serum cholesterol levels or with the risk for coronary artery disease, but did seem to be related to cholesterol levels in the cerebrospinal fluid. [OMIM:ATP-BINDING CASSETTE, SUBFAMILY A, MEMBER 2; ABCA2]
common on affy axiom data
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The C allele of rs1937 appears to be protective against late-onset Alzheimer's disease in Han Chinese.
common in clinvar
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Presenile dementia and cerebral haemorrhage linked to a mutation at codon 692 of the beta-amyloid precursor protein gene. Presenile Alzheimer dementia characterized by amyloid angiopathy and large amyloid core type senile plaques in the APP 692Ala-->Gly mutation. Flemish and Dutch mutations in amyloid beta precursor protein have different effects on amyloid beta secretion. Presentation of amyloidosis in carriers of the codon 692 mutation in the amyloid precursor protein gene (APP692). In vitro studies of amyloid beta-protein fibril assembly and toxicity provide clues to the aetiology of Flemish variant (Ala692-->Gly) Alzheimer's disease. [OMIM:?]
common in complete genomics
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rs63751141, also known as C92S or Cys92Ser, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63751141(C) allele is considered causative for early-onset Alzheimer's disease. [OMIM:?]
common in clinvar
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rs63751223, also known as A426P or Ala426Pro, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63751223(C) allele is considered causative for early-onset Alzheimer's disease. [OMIM:?]
common in clinvar
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rs63751235, also known as L286V or Leu286Val, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63751235(G) allele is considered causative for early-onset Alzheimer's disease. [OMIM:?]
1 genoset 123 snps
(hide) Amyloidosis
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs76992529, also known as V122I, Val122Ile, V142I or Val142Ile, is a mutation in the transthyretin TTR] gene. This risk allele for this SNP, rs76992529(A), is found primarily in people of African ancestry, and may be found in up to 4% of African-Americans. A person with one or two copies of the (A) allele of this SNP is at significantly higher (by about 2 - 3 fold) risk of developing cardiac amyloidosis, in which levels of the transthyretin protein build up and can lead to heart failure, especially with increasing age. This SNP is also known as i3002759 and i6019130 within 23andMe data. Letter: Diagnosis of neuronal ceroid lipofuscinosis by electron microscopy of urinary sediment. Cardiac amyloidosis: report of a patient heterozygous for the transthyretin isoleucine 122 variant. The V122I ...
2 snps
(hide) Amyotrophic Lateral Sclerosis
Magnitude: 2
Frequency: 19.5%
Repute:Bad
References:10
Frequency: 19.5%
Repute:Bad
References:10
1.60x risk of developing ALS
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rs10260404, a SNP in the region of the DPP6 gene on chromosome 7, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The overall odds ratio for the risk allele rs10260404(C) is 1.30 (CI: 1.18-1.43, p=0.017). When broken down by genotype, the odds ratios for heterozygotes are 1.20 (CI: 1.06-1.41), and for rs10260404(C;C) homozygotes, 1.60 (CI: 1.32-1.92). A 'C-C' haplotype for this SNP and that of it's neighbor rs10239794 is also highly (statistically; p=10e-9) associated with ALS. However, in an expanded study pooling 4 populations (Irish, Dutch, US, Polish) rs10260404 failed to reach Bonferroni significance. although it did remain significant in the (expanded) Irish-only population. [PharmGKB:Non-Curated GWAS results: Screening...
Frequency: 8.0%
References:4
References:4
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[PharmGKB:Non-Curated GWAS results: Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data (Initial Sample Size: 276 cases, 276 controls; Replication Sample Size: NR). This variant is associated with Amyotrophic lateral sclerosis.] [GWAS:Amyotrophic lateral sclerosis]
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[PharmGKB:Non-Curated GWAS results: Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data (Initial Sample Size: 276 cases, 276 controls; Replication Sample Size: NR). This variant is associated with Amyotrophic lateral sclerosis.] [GWAS:Amyotrophic lateral sclerosis]
1.7x increased risk for ALS
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rs6690993 is one of 6 SNPs found upstream of an (uncharacterized) gene known as FLJ10986 that have been found to be overrepresented in patients with sporadic amyotrophic lateral sclerosis (ALS). A genome-wide association study of 1,152 ALS patients determined an allelic odds ratio of 1.35 for the rs6690993(G) allele (CI: 1.13-1.62, p=3x10<sup>-4</sup>). This association was seen only in Caucasians upon replication and not in non-Caucasians. The genotypic odds ratio presented were 1.69 (CI: 1.16-2.47) and 1.2 (CI: 0.81-1.71) for homozygotes and heterozygotes, respectively. * Note: this SNP is in strong linkage disequilibrium with rs6700125 (r<sup>2</sup>>0.8) A study involving a large case-control series from the Netherlands, Belgium, Sweden and Ireland (total: 18...
1.76x increased risk for ALS
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rs6700125 is one of 6 SNPs found upstream of an (uncharacterized) gene known as FLJ10986 that have been found to be overrepresented in patients with sporadic amyotrophic lateral sclerosis (ALS). A genome-wide association study of 1,152 ALS patients determined an allelic odds ratio of 1.38 for the rs6700125(T) allele (CI: 1.16-1.65, p=0.00032). The genotypic odds ratio presented were 1.76 (CI: 1.22-2.55) and 1.2 (CI: 0.83-1.73) for homozygotes and heterozygotes, respectively. * Note: this SNP is in strong linkage disequilibrium with rs6690993 (r<sup>2</sup>>0.8) A study involving a large case-control series from the Netherlands, Belgium, Sweden and Ireland (total: 1883 sporadic ALS patients and 2063 controls) found no significant association between sporadic ALS and the six p...
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[GWAS:Amyotrophic lateral sclerosis]
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This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
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[GWAS:Amyotrophic lateral sclerosis]
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[PharmGKB:Non-Curated GWAS results: Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data (Initial Sample Size: 276 cases, 276 controls; Replication Sample Size: NR). This variant is associated with Amyotrophic lateral sclerosis.] [GWAS:Amyotrophic lateral sclerosis]
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[GWAS:Amyotrophic lateral sclerosis]
Frequency: 16.1%
References:1
References:1
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[GWAS:Amyotrophic lateral sclerosis]
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rs4630362 is one of several TXNRD1 SNPs significantly associated with familial amyotrophic lateral sclerosis (FALS) but not sporadic amyotrophic lateral sclerosis (ALS).
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rs6539137 is one of several TXNRD1 SNPs significantly associated with familial amyotrophic lateral sclerosis (FALS) but not sporadic amyotrophic lateral sclerosis (ALS). The risk allele, rs6539137(A), is also associated with an earlier age of onset by 8 years, and the shift was more significant in males (in fact, insignificant in females).
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[PharmGKB:Non-Curated GWAS results: Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data (Initial Sample Size: 276 cases, 276 controls; Replication Sample Size: NR). This variant is associated with Amyotrophic lateral sclerosis.] [GWAS:Amyotrophic lateral sclerosis]
Frequency: 23.0%
References:1
References:1
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[GWAS:Amyotrophic lateral sclerosis]
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[GWAS:Amyotrophic lateral sclerosis]
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[GWAS:Amyotrophic lateral sclerosis]
Frequency: 31.9%
References:1
References:1
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[GWAS:Amyotrophic lateral sclerosis]
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[GWAS:Amyotrophic lateral sclerosis]
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This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
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[GWAS:Amyotrophic lateral sclerosis]
Normal risk for ALS
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rs3825776, a SNP in the region of the LIPC gene on chromosome 15, has been associated with the sporadic form of ALS (Lou Gehrig's disease) in a study of 1000+ European patients. The odds ratio for the risk allele rs3825776(G) is 1.34 (CI: 1.12 - 1.46).
Frequency: 40.6%
References:1
References:1
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This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
Frequency: 41.6%
References:1
References:1
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[GWAS:Amyotrophic lateral sclerosis]
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[GWAS:Amyotrophic lateral sclerosis]
Frequency: 44.2%
References:8
References:8
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rs12608932 is a SNP located in an intron of the UNC13A gene which encodes UNC13A, a protein involved with regulation of neurotransmitters like glutamate at central and neuromuscular synpases. rs12608932(C, reference allele: A) was identified as a risk allele associated with sporadic amyotrophic lateral sclerosis (sALS) or Lou Gehrig’s disease in a two-stage association study with individuals of European ancestry. An initial genome-wide study (2,323 case and 9,013 control subjects) identified SNPs that exhibited P-values less than 1.0x10-4, including rs12608932 (P =1.30x10-9, OR=1.25). These SNPs were further evaluated in a second, independent cohort of individuals (2,532 affected individuals and 5,940 controls). This SNP exhibited significant association in the replication round (P=1...
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[GWAS:Amyotrophic lateral sclerosis]
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[GWAS:Amyotrophic lateral sclerosis]
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[GWAS:Amyotrophic lateral sclerosis]
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homozygosity for the favorable allele (CC) associated with a 14 month survival advantage in ALS patients. further analysis (sequence, genotypic, and functional) showed LD between rs1541160 and rs522444 and that favorable alleles correlate with reduced KIFAP3 expression. However, a later study attempting to replicate these findings in a population-based cohort of 500 Italian ALS patients could not find any effect on either survival or gene expression based on any SNPs (including rs1541160) from the KIFAP3 locus. [OMIM:?]
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[GWAS:Amyotrophic lateral sclerosis]
Frequency: 52.3%
References:1
References:1
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This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
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[GWAS:Amyotrophic lateral sclerosis]
(hide)
This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
Frequency: 54.0%
References:1
References:1
(hide)
[GWAS:Amyotrophic lateral sclerosis]
(hide)
This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
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Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia. Usefulness of direct sequencing of pooled DNA for SNP identification and allele-frequency determination compatible with a common disease/common variant hypothesis. Publicly Available Single Nucleotide Polymorphisms in Genes Possibly Susceptible to Antiepileptic Drug Resistance in Healthy Koreans Development of a high-throughput microarray-based resequencing system for neurological disorders and its application to molecular genetics of amyotrophic lateral sclerosis.
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.0000006; OR: 5.4 (1.9, 17.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Amyotrophic lateral sclerosis]
Frequency: 58.4%
References:4
References:4
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[PharmGKB:Non-Curated GWAS results: Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data (Initial Sample Size: 276 cases, 276 controls; Replication Sample Size: NR). This variant is associated with Amyotrophic lateral sclerosis.] [GWAS:Amyotrophic lateral sclerosis]
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[GWAS:Amyotrophic lateral sclerosis]
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[GWAS:Amyotrophic lateral sclerosis]
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The common form at this site in most populations is rs11701(T), and the variant form is rs11701(G). Having at least one copy of this variant form, rs11701(G), has been associated with an increased incidence of ALS in Scottish and Irish populations studied, but not in populations from the U.S., Sweden, or England. *rs11701 In Irish amyotrophic lateral sclerosis patients, there was a significant allelic association with the rs11701 SNP & a new mutation (K40I) that potentially inhibits angiogenin function. [OMIM:ANGIOGENIN; ANG]
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[GWAS:Amyotrophic lateral sclerosis]
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[GWAS:Amyotrophic lateral sclerosis]
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rs333662 is one of 6 SNPs found upstream of an (uncharacterized) gene known as FLJ10986 that have been found to be overrepresented in 1,152 patients with sporadic amyotrophic lateral sclerosis (ALS). A study involving a large case-control series from the Netherlands, Belgium, Sweden and Ireland (total: 1883 sporadic ALS patients and 2063 controls) found no significant association between sporadic ALS and the six previously reported associated SNPs, including this one.
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[GWAS:Amyotrophic lateral sclerosis]
References:1
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rs10861192 is one of several TXNRD1 SNPs significantly associated with familial amyotrophic lateral sclerosis (FALS) but not sporadic amyotrophic lateral sclerosis (ALS).
References:1
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According to , variations at rs12704795, originally known as rs17876088, located in an intron of the PON2 gene, appear to modulate both susceptibility to, and protection from, the sporadic form of ALS (Lou Gehrig's disease). Paraoxonase 2 (PON2) polymorphisms and development of renal dysfunction in type 2 diabetes: UKPDS 76. Evaluation of polymorphisms in paraoxonase 2 (PON2) gene and their association with cardiovascular-renal disease risk in Mexican Americans. Association analysis of PON2 genetic variants with serum paraoxonase activity and systemic lupus erythematosus.
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[GWAS:Amyotrophic lateral sclerosis]
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This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
Magnitude: 0
Frequency: 60.2%
Repute:Good
References:1
Frequency: 60.2%
Repute:Good
References:1
common in complete genomics
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This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
normal
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rs2814707 is one of 2 SNPs from the ch 9p21.2 region associated in a large GWAS study with ALS risk, the other SNP being rs3849942. In this study, the reported odds ratio for rs2814707(A) was 1.22 (CI: 1.15 - 1.30, p = 4.72 x 10e-10). The odds ratio for the minor rs2814707(A) allele was 1.16 (p=7.45x10e-9). 23andMe blog rs2814707(T) 1.16x odds of ALS rs12608932(C) 1.2x odds of ALS [PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000002; OR: 5.2 (1.8, 16.7)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [OMIM:?]
normal
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rs3849942 is one of 2 SNPs from the ch 9p21.2 region associated in a large GWAS study with ALS risk, the other SNP being rs2814707. In this study, the reported odds ratio for rs3849942(A) was 1.22 (CI: 1.15 - 1.30, p = 4.64 x 10e-10). The odds ratio for the minor rs3849942(A) allele was 1.15 (p=1.01x10e-8). From a study of 405 Finnish patients with ALS, rs3849942 was found within a 42 SNP haplotype associated with highly increased (p = 7 x 10e-33) risk when patients with familial ALS were compared to controls (odds ratio of 21.0, CI: 11.2-39.1). This haplotype overlapped with a region reported (by others) to associate with risk for frontotemporal dementia. In terms of population attributable risk, for the 93 patients with familial ALS, this 9p21 locus accounts for 38% and that of rs1304801...
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This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
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[PharmGKB:Non-Curated GWAS results: ITPR2 as a susceptibility gene in sporadic amyotrophic lateral sclerosis: a genome-wide association study (Initial Sample Size: 737 cases, 721 controls; Replication Sample Size: 1,030 cases, 1,195 controls). This variant is associated with Amyotrophic lateral sclerosis.] [GWAS:Amyotrophic lateral sclerosis]
common in complete genomics
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Associated with risk of amyotrophic lateral sclerosis (ALS) in two European populations [OMIM:GRANULIN PRECURSOR; GRN]
Magnitude: 0
Frequency: 87.6%
References:1
Frequency: 87.6%
References:1
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[GWAS:Amyotrophic lateral sclerosis]
Magnitude: 0
Frequency: 91.9%
Repute:Good
References:1
Frequency: 91.9%
Repute:Good
References:1
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23andMe blog 2x risk of ALS Chromogranin B P413L variant as risk factor and modifier of disease onset for amyotrophic lateral sclerosis. The P413L chromogranin B variation in French patients with sporadic amyotrophic lateral sclerosis.
63 snps
(hide) Aneurysm
Magnitude: 2
Frequency: 50.0%
Repute:Bad
References:77
Frequency: 50.0%
Repute:Bad
References:77
1.3x risk for Heart Attack. Normal risk for Abdominal Aortic Aneurysm and Brain Aneurysm. One copy of an SNP that increases risk of Myocardial Infarction (Heart Attack) and other Coronary Heart Disease. It has been shown that regularly eating raw vegetables and fruit can reduce the risk to the same level as people without this SNP. This SNP also has the normal medium risk of abdominal aortic aneurysm (weakened artery to abdomen and legs) or brain aneurysm (weakened artery to brain).
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This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...
increased risk for heart disease
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discussed in this blog post as possibly playing a role in coronary heart disease This SNP was also associated with increased risk for coronary artery disease in a Korean population. The association remained significant after adjusting for significant clinical covariates (P=0.001 to 0.024). We identified one risk haplotype (GGGG; P=0.017) and one protective haplotype (AAAA; P=0.007) for development of CAD. Further analysis suggested that the SNPs probably confer susceptibility to CAD in a dominance model (covariates-adjusted P=0.001 to 0.024; OR=2.37 to 1.54). Also found to be significant in a study of 416 Italian myocardial infarction patients. Found to be associated with coronary heart disease in a study of 1360 Chinese Han patients, with an odds ratio of 1.52 (CI: 1.13 - 2.04) for rs2383...
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Based on a large study (~6,000 cases and 14,000 controls) of both European and Japanese populations, the rs9298506(A) allele has been associated with higher risk of aneurysm, with an odds ratio per allele of 1.28 (CI:1.20-1.38, p=1.0e-06). Brain Aneurysm [PharmGKB:Non-Curated GWAS results: Susceptibility loci for intracranial aneurysm in European and Japanese populations. (Initial Sample Size: 1,580 European cases, 6,276 European controls; Replication Sample Size: 495 Japanese cases, 676 Japanese controls); (Region: 8q11.23-q12.1; Reported Gene(s): SOX17; Risk Allele: rs9298506-A); (p-value= 0.000000002).This variant is associated with Intracranial aneurysm.] [OMIM:?] [GWAS:Intracranial aneurysm]
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Brain Aneurysm
Normal risk of aneurysm
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23andMe blog aneurysm *rs700651 2 G 1.18x risk 1.56x risk *rs10958409 8 A 1.37x risk 1.79x risk *rs1333040 9 T 1.29x risk 1.67x risk Increased risk of intracranial (brain aneurysm) with certain SNPs. rs700651(G;G) associated with 1.56x risk of developing an intracranial aneurysm (IA). Heterozygote risk is 1.18x. Other SNPs associated with increased risk of developing IA include rs1333040 and rs10958409. rs10958409 is located on chromosome 9; rs1333040 is located on chromosome 8; rs700651 is located on chromosome 2. Unfortunately, the first sign of an intracranial aneurysm is rupture. Catastrophic bleeding and death may result. Specific knowledge of risk may influence screening decision. More information: Intracranial aneurysm screening: indications and advice for practice. . [PharmGKB:Non...
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Brain Aneurysm
Frequency: 56.6%
References:1
References:1
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Based on a large study (~6,000 cases and 14,000 controls) of both European and Japanese populations, the rs11661542(C) allele has been associated with higher risk of aneurysm, with an odds ratio per allele of 1.22 (CI: 1.15-1.28, p=1.1e-12). [OMIM:?]
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[GWAS:Intracranial aneurysm]
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Brain Aneurysm
1.24x increased myocardial infarction risk, 1.29x increased aneurysm risk
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A common variant on chromosome 9p21 affects the risk of myocardial infarction, and is further discussed in this blog post 23andMe blog aneurysm *rs700651 2 G 1.18x risk 1.56x risk *rs10958409 8 A 1.37x risk 1.79x risk *rs1333040 9 T 1.29x risk 1.67x risk Brain Aneurysm [PharmGKB:Non-Curated GWAS results: Susceptibility loci for intracranial aneurysm in European and Japanese populations. (Initial Sample Size: 1,580 European cases, 6,276 European controls; Replication Sample Size: 495 Japanese cases, 676 Japanese controls); (Region: 9q21.3; Reported Gene(s): CDKN2A, CDKN2B; Risk Allele: rs1333040-T); (p-value= 0.0000000001).This variant is associated with Intracranial aneurysm.] [OMIM:ANEURYSM, INTRACRANIAL BERRY, 6] [GWAS:Intracranial aneurysm]
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Based on a large study (~6,000 cases and 14,000 controls) of both European and Japanese populations, the rs9315204(T) allele has been associated with higher risk of aneurysm, with an odds ratio per allele of 1.20 (CI: 1.13-1.28, p=2.5e-09). [OMIM:?]
Magnitude: 0
Frequency: 69.9%
References:7
Frequency: 69.9%
References:7
normal
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23andMe blog aneurysm *rs700651 2 G 1.18x risk 1.56x risk *rs10958409 8 A 1.37x risk 1.79x risk *rs1333040 9 T 1.29x risk 1.67x risk Brain Aneurysm [PharmGKB:Non-Curated GWAS results: Susceptibility loci for intracranial aneurysm in European and Japanese populations. (Initial Sample Size: 1,580 European cases, 6,276 European controls; Replication Sample Size: 495 Japanese cases, 676 Japanese controls); (Region: 8q11.23; Reported Gene(s): SOX17; Risk Allele: rs10958409-A); (p-value= 0.0000000001).This variant is associated with Intracranial aneurysm.] [OMIM:ANEURYSM, INTRACRANIAL BERRY, 10] [GWAS:Intracranial aneurysm]
Magnitude: 0
Frequency: 85.8%
References:4
Frequency: 85.8%
References:4
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Based on a large study (~6,000 cases and 14,000 controls) of both European and Japanese populations, the rs12413409(G) allele has been associated with higher risk of aneurysm, with an odds ratio per allele of 1.29 (CI:1.19-1.40, p=1.2e-09). Also: 23andMe blog blood pressure Coronary Heart Disease High Blood Pressure (Hypertension) [OMIM:?] [GWAS:None]
13 snps
(hide) Angioedema
normal This genotype is susceptible to skin swelling when taking medicines called ACE Inhibitors . for more information visit rs3788853
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A form of this snp, located upstream of the XPNPEP2 gene on the X chromosome, may cause susceptibility to skin swelling when taking medicines called ACE Inhibitors. Also known as -2399C/A in the literature; however in SNPedia, where the orientation of the corresponding dbSNP entry is recognized as primary, this is G/T. After noticing the association of this SNP with the phenotype, the authors genotyped 20 independent AE-ACEi cases and 60 unrelated, matching controls for this SNP. The T allele was present in 8 of the 20 AE patients; and by allele counting, the T allele was found at a frequency of 11.1% in the control population and 27.3% in their AE-ACEi cases. *See also OMIM 300145 [OMIM:?]
1 snp
(hide) Ankylosing spondylitis
4.6x increased risk of Ankylosing Spondylitis. Substantially increased (but still only 0.5%) risk of this rare autoimmune disease that causes inflammation of the spine and joints. Based on preliminary research. Age of onset is usually between 15 and 25, so if you are older than that, there's not much need for worry.
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Each A allele at rs7743761 is associated with 4.6x higher risk of ankylosing spondylitis, according to a 2007 publication. [GWAS:Ankylosing spondylitis]
Magnitude: 2
Frequency: 38.9%
Repute:Bad
References:40
Frequency: 38.9%
Repute:Bad
References:40
1.5x increased risk for certain autoimmune diseases; 2x increased risk for Graves disease
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SNP rs10889677, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele for this SNP has been associated with increased risk for ankylosing spondylitis in a large study of over 1,000 Caucasian patients. The odds ratio is 1.3 (p=1.3x10e-6). In a study of 216 North American patients with Graves' disease, the C allele of rs10889677 was 2.03x overrepresented (p=1.3x10<sup>–4</sup>), and the homozygous rs10889677(C;C) genotype was also overrepresented (2.36x; p=1.4x10<sup>-4</sup>) in Graves ophthalmopathy patients. A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ance...
Normal risk (0.1%) for Ankylosing Spondylitis. Normal, very low risk of the rare autoimmune disease that causes inflammation of the spine and joints. Based on preliminary research.
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Each A allele at rs2303138 in the LNPEP gene is associated with 1.5x higher odds of ankylosing spondylitis, according to a 2007 report.
1.4x higher risk for Ankylosing Spondylitis. Higher, but still very low, risk (0.14%) of this rare autoimmune disease that causes inflammation of the spine and joints.
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rs30187 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. Each T allele appears to increase the odds by about 1.4x (p=3.4x10e-10). A study of 872 Korean patients found that each T allele was associated with 1.5x higher odds of ankylosing spondylitis. [GWAS:None]
Magnitude: 1.3
Frequency: 55.8%
Repute:Good
References:9
Frequency: 55.8%
Repute:Good
References:9
Normal risk (about 0.1%) for Ankylosing Spondylitis. Normal, but still very low, risk (1 in a thousand) of the rare autoimmune disease that causes inflammation of the spine and joints. Based on preliminary research.
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rs10050860 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.71 (p=7.7x10e-9). Note that the text description (but not the result) at 23andMe is wrong. It is the uncommon T allele that gives protection. Association of an ERAP1 ERAP2 haplotype with familial ankylosing spondylitis. Investigating the genetic association between ERAP1 and ankylosing spondylitis. Serum cytokine receptors in ankylosing spondylitis: relationship to inflammatory markers and endoplasmic reticulum aminopeptidase polymorphisms. ERAP1 polymorphisms and haplotypes are associated with ankylosing spondylitis susceptibility and functional severity in a Spanish population. Associations between ERAP1...
Magnitude: 1.1
Frequency: 91.8%
Repute:Bad
References:100
Frequency: 91.8%
Repute:Bad
References:100
Normal, but higher risk for certain autoimmune diseases. Almost everyone has this form, but it indicates a slightly higher risk of Ankylosing Spondylitis, Crohn's Disease (1.09x), Psoriasis (1.06x), and Ulcerative Colitis (1.06x). The risk is much greater than for the rare version. This is the interleukin-23 (IL-23) receptor. Media:http://www.the-rheumatologist.org/details/article/2528901/Neutralizing_IL-23_and_Its_Targets_May_Improve_Ankylosing_Spondylitis.html] Neutralizing IL-23 and Its Targets May Improve Ankylosing Spondylitis by Lara C. Pullen, PhD in The Rheumatologist newsmagazine ]
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A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-1....
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According to a 2007 report, each G allele at rs7302230 in the CLSTN3 gene is associated with 1.6x higher odds of ankylosing spondylitis.
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[GWAS:Ankylosing spondylitis]
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[OMIM:?] [GWAS:Ankylosing spondylitis]
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23andMe reports that the GG genotype at rs2242944 is associated with 1.4x higher odds of ankylosing spondylitis, and the AA genotype is associated with 0.7x lower odds. Association of the intergenic single-nucleotide polymorphism rs10865331 (2p15) with ankylosing spondylitis in a Spanish population. [OMIM:?] [GWAS:Ankylosing spondylitis]
1.5x risk
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SNP rs1004819, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele is also reported to increase the risk for developing ankylosing spondylitis, based on a large study of over 1,000 Caucasian patients. The odds ratio is 1.2 (p=8.8x10e-5). significant associations with rs1004819, rs7517847, and rs11209026. Having any CARD15 variant was associated with a significant risk for CD (P < 0.0001). Investigation of the IL23R gene in a Spanish rheumatoid arthritis cohort. rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and OCTN1/2 variants. CARD15 and IL23R influences Crohn's disease susceptibility but not disease phenotype in a Brazili...
Frequency: 41.4%
Repute:Bad
References:28
Repute:Bad
References:28
1.3x higher risk for spondylitis
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rs11209032 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 1.3 (p=7.5x10e-9). rs11209032 and rs1495965 no significant association with systemic sclerosis [OMIM:?]
1.2x higher risk for spondylitis
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rs1495965 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 1.2 (p=6.6x10e-6). 23andMe reports that the CC genotype at rs1495965 is associated with 1.56x higher odds of Behçet's disease, and the TT genotype with 0.64x lower odds, than the CT genotype. rs11209032 and rs1495965 no significant association with systemic sclerosis A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Investigation of the IL23R gene in a Spanish rheumatoid arthritis cohort. rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and OCTN1/2 variants. CARD15 and IL23R influences Croh...
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A study of 201 Canadian ankylosing spondylitis families concluded the ALPL (TNAP) haplotype G-G-T for SNPs rs3767155-rs3738099-rs1780329, respectively, is significantly associated with the disease but only in men. A study of 353 Chinese ankylosing spondylitis patients found no significant difference in allele, genotype or haplotype frequencies for this SNP in either case-control or family-based association studies, which indicated that the TNAP (also known as ALPL) gene is unlikely to play a major role in the susceptibility to ankylosing spondylitis in the Chinese Han population.
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[OMIM:?] [GWAS:Ankylosing spondylitis]
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Allelic variants of IL1R1 gene associate with severe hand osteoarthritis. [OMIM:?] [GWAS:Ankylosing spondylitis]
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A study of 201 Canadian ankylosing spondylitis families concluded the ALPL (TNAP) haplotype G-G-T for SNPs rs3767155-rs3738099-rs1780329, respectively, is significantly associated with the disease but only in men. A study of 353 Chinese ankylosing spondylitis patients found no significant difference in allele, genotype or haplotype frequencies for this SNP in either case-control or family-based association studies, which indicated that the TNAP (also known as ALPL) gene is unlikely to play a major role in the susceptibility to ankylosing spondylitis in the Chinese Han population.
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A study of 201 Canadian ankylosing spondylitis families concluded the ALPL (TNAP) haplotype G-G-T for SNPs rs3767155-rs3738099-rs1780329, respectively, is significantly associated with the disease but only in men. A study of 353 Chinese ankylosing spondylitis patients found no significant difference in allele, genotype or haplotype frequencies for this SNP in either case-control or family-based association studies, which indicated that the TNAP (also known as ALPL) gene is unlikely to play a major role in the susceptibility to ankylosing spondylitis in the Chinese Han population.
normal risk
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rs27044 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 1.40 (p=1.0x10e-6). A study of 872 Korean patients with ankylosing spondylitis also found a significant association with this SNP.
Magnitude: 0
Frequency: 48.7%
References:8
Frequency: 48.7%
References:8
normal risk ankylosing spondylitis
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rs10865331 is a SNP in chromosomal region 2p15. After initial GWAS reports linked this SNP to ankylosing spondylitis (AS), a follow-up study in 456 Spanish patients replicated the association between the rs10865331(A) allele and higher risk for AS (p = 0.039). In a 2010 report, the AA genotype was associated with 1.3x odds of ankylosing spondylitis, and the GG genotype with 0.8x odds, compared to the AG genotype. [OMIM:?] [GWAS:Ankylosing spondylitis]
normal risk
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rs1343151 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.8 (p=1.0x10e-5). rs1343151 with rheumatoid arthritis (OR=1.14 [1.06-1.22], P=4x10-4) rs1343151 was '''not''' associated with rheumatoid arthritis in a study of 1,200+ Korean patients. A;A homozygous individuals showed a strongly reduced risk of Crohn's Disease compared those who were G;G homozygous. [PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This v...
Magnitude: 0
Frequency: 58.0%
References:11
Frequency: 58.0%
References:11
0.76x lower risk for spondylitis
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rs17482078 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.70 (p=1.2x10e-8). [GWAS:Behcet's disease]
normal risk
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rs2287987 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.71 (p=1.0x10e-8).
common in complete genomics
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23andMe reports that each G allele at rs868213 appears to be associated with 1.5x higher odds of ankylosing spondylitis.
Magnitude: 0
Frequency: 91.1%
Repute:Bad
References:28
Frequency: 91.1%
Repute:Bad
References:28
normal risk
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rs11465804 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.68 (p=0.0002). [PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease] [GWAS:Crohn's disease]
26 snps
(hide) Anorexia nervosa
A1/A2: Bad at avoidance of errors. 0.5x lower OCD risk, 0.87x lower Tardive Diskinesia risk, higher ADHD risk. More Alcohol Dependence. Lower risk of Postoperative Nausea. Increased obesity. Bupropion is not effective. The DRD2 TaqIA A1/A2 version causes less dopamine receptors. Doesn't learn from mistakes well. Reduced response to errors and increased addictive behavior Men may have half the risk of Obsessive Compulsive Disorder but higher risk of ADHD. Women have lower Persistence. 0.87x reduced risk of Tardive Diskinesia when taking dopamine receptor antagonists. Slightly increased risk of alcoholism and smoking addiction. Slower recovery from traumatic brain injury. Lower risk of postoperative nausea within 6 hours of surgery. Bupropion (Wellbutrin, Budeprion, Prexaton, Elontril, Aple...
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain . Reduced response to errors and increased addictive behavior It has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessa...
more resistant to treatment for depression
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Based on a study of 256 Caucasian patients being treated for depression, carriers of a rs1049353(G) allele were less likely to respond favorably, particularly if they were females with comorbid anxiety. rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. No evidence for an involvement of variants in the cannabinoid receptor gene (CNR1) in obesity in German children and adolescents. The G1422A variant of the cannabinoid receptor gene (CNR1) is associated with abdominal adiposity in obese men. No association of...
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[GWAS:Anorexia nervosa]
Frequency: 46.0%
References:1
References:1
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[GWAS:Anorexia nervosa]
Frequency: 68.1%
References:1
References:1
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[GWAS:Anorexia nervosa]
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rs533123 is a SNP in the opioid receptor, delta 1 OPRD1 gene. A genome-wide association study of 1,000+ European anorexia nervosa patients (and 3,700+ pediatric controls) concluded that rs533123 was significantly (p = 0.0015) associated with the disorder when analyzed specifically, however the finding did not reach genome-wide significance.
normal
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rs324420 is a SNP, also known as Pro129Thr, in the fatty acid amide hydrolase FAAH gene, which has shown associations with some substance use disorders. rs324420(C) encodes the more common Pro, while the (A) allele encodes the Thr. Among 80 individuals with drug abuse or alcoholism and over 1,000 controls, the odds ratio for risk of problem drug or alcohol use among rs324420(A;A) individuals was 4.5 (CI: 2.2 - 8.4); the odds ratio for risk of street drug use was 2.2 (CI: 1.3–3.7); and the odds ratio for risk of combined street drug use and problem drug/alcohol use was 4.9 (CI: 2.5–9.7) When this study was pooled with the results of another study of 249 subjects with documented multiple different drug addictions compared to drug free individuals of the same ethnic backgrounds, t...
common/normal Val/val (normal) variant of the Val66Met snp in the BDNF gene that codes for brain-derived neurotrophic factor. Met/met is associated with susceptibility to neuropsychiatric disorders.
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
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[GWAS:Anorexia nervosa]
11 snps
(hide) Anxiety disorder
normal
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rs4570625, also known as G-703T, is a SNP in the tryptophan hydroxylase 2 TPH2 gene. This SNP has been linked to several psychiatric and/or behavioural phenomena, including: * rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder * rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission * rs4570625(G;G) homozygosity was a significant predictor of clinical placebo response, being associated with greater improvement in anxiety symptoms. g2b2mh is rs4570625(G;G) is a significant predictor of clinical placebo response? maybe not panic disorder with a possible gender-dependent effect Transmission disequilibrium of polymorphic variants in the tryptophan hydroxylase-2 gene in attention-deficit/hyperactivity disorder. Associa...
more anxious females, less anxious males
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rs6330 is a SNP causing a change in an amino acid in the nerve growth factor ([NGF]) gene, and based on this, it is also known as 104C>T or Ala35Val. The more common (C) allele encodes the alanine (Ala). A study of 337 (age: 39.2 +/- 14.6 years) unrelated subjects of German descent found a significant (p=0.011) gender-dependent effect of this SNP on anxiety related personality traits. rs6330(C;C) females had higher levels of trait anxiety than (C;T) or (T;T) females, while the opposite effect was seen in males.
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part of a three marker haplotype rs737865-rs4680-rs165599 COMT haplotypes at rs737865 and rs165599 may predict a favorable outcome for bupropion treatment for smoking cessation. We have typed the IVS 1 rs737865 and 3' rs615599 sites and also included a novel IVS 1 indel polymorphism. We report that the schizophrenia-associated haplotype is significantly heterogeneous in populations worldwide. may affect non-Hodgkin lymphoma, anxiety-related personality traits Also mentioned in these PMIDs * * * * * * [PharmGKB:Curated This variant may predict a favorable outcome for bupropion treatment for smoking cessation] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism.
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism.
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism.
References:1
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism.
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anxiety-related personality traits, ADHD, schizophrenia part of a three marker haplotype rs737865-rs4680-rs165599 epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes popular in pubmed is associated with bipolar disorder and influences prefrontal aspects of verbal memory in bipolar patients and healthy controls. [PharmGKB:Curated In a study of 78 African American and 65 white patients diagnosed with schizophrenia or schizoaffective disorder, this SNP in the COMT gene was found to have significant associations with response to risperidone over 2-12 weeks in both African-American and white patients.] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism. Associations of glutamate decarboxylase genes with initial sensitivity and age-at-onset of alcohol dependence in the Irish Affected Sib Pair Study of Alcohol Dependence. Heroin addiction in African Americans: a hypothesis-driven association study.
complex; possible association with anxiety related behaviours
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In mice, the genetic locus best correlated to anxiety-related behaviour contains the 'regulator of G protein signaling 2' gene . In humans, SNPs in the equivalent RGS2 gene have now been studied to see if they are correlated to anxiety related disorders. In the first part of one study, 119 families including children underwent standard lab-based behavioural assessments of behavioural inhibition, defined as a heritable temperamental profile characterized by a tendency to be shy, avoident, and behaviourally restrained in situations that are novel or unfamiliar. Along with some other RGS2 SNPs, carriers of a rs4606(G) allele were 3 fold more likely to exhibit behavioural inhibition (CI: 1.31-6.84, p = 0.0026). In the second part of this study, 744 college undergraduates (228 men, 516 women) w...
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism.
11 snps
(hide) Arthritis
Frequency: 53.8%
Repute:Bad
References:21
Repute:Bad
References:21
1.4x increased risk for rheumatoid arthritis
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rs10818488, a SNP located in between the C5 and TRAF1 genes, was identified as the SNP from this region showing maximal association with rheumatoid arthritis in a study of ~2000 Dutch, Swedish, and American patients. This study also reported that this SNP was significantly (p = 0.008) associated with increased disease progression as determined by radiographic damage over time in rheumatoid arthritis patients. The risk allele for rs10818488 is the minor allele, (A). If (and as) reported from just the Dutch RA patients, the odds ratio associated with rs10818488(A;G) heterozygotes is 1.38 (CI 1.04-1.83, p = 0.027) and with rs10818488(A;A) homozygotes 2.06 (95% CI 1.42-2.98, p = 1.29E-3). Combining data from all 2,000 patients, the odds ratio associated with rs10818488(A) is 1.26 (CI 1.15-1.37...
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rs3806265 was associated with juvenile idiopathic arthritis based on a study of 950 Caucasian patients.
1.7x risk for RA; 1.6X for T1D; also MS?
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rs2104286 has also been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.30 (CI 1.02-1.65), and for homozygotes, 1.57 (CI 1.25-1.99). The same (A) allele of rs2104286, which is located in the first intron of the IL2RA gene, was calculated to confer a slight increase (19%) in the risk of developing multiple sclerosis. [PMID tbd; NEJM 357, 29 July 2007, DA Hafler et al.] Note that the (A) allele is the most common at this position in all known populations. blog post giving perspective on the significance of this SNP with respect to multiple sclerosis news announcement rs2104286 was significantly associated with UK cases of juvenile idiopathic arthritis (JIA)(allelic odds ra...
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y or Cys282Tyr mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who act...
common in complete genomics appears to be common on the 23andMe platform
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rs2066845 is a SNP in the NOD2 gene; this SNP is also known as G908R or Gly908Arg, with the (G) allele encoding the Gly (G) and the (C) allele encoding the Arg (R). The two initial reports linking the minor(C) allele as strongly associated with Crohn's disease are and . rs2066845 has also been reported, with an odds ratio of 3.5 (CI 1.51–7.01), to be associated with psoriatic arthritis. No association was found for NOD2/CARD15 SNPs (R702W, G908R) in Chinese patients with inflammatory bowel disease. [OMIM:CROHN DISEASE, SUSCEPTIBILITY TO]
5 snps
(hide) Asian flush
Alcohol Flush: Normal, doesn't flush. Normal hangovers. Normal risk of Alcoholism. Normal risk of Esophageal Cancer. Disulfiram is effective for alcoholism. Two working copies of Aldehyde Dehydrogenase (ALDH2) mean you won't turn bright red when you drink alcohol, unlike most Asians. After your body turns alcohol into the dangerous acetaldehyde, this gene quickly turns the acetaldehyde into vinegar. It also stops the acetaldehyde in cigarettes from causing Esophageal Cancer. It reduces hangovers compared to Asians, but less hangovers and flushing obviously increases the risk of alcoholism. Alcoholism can be treated effectively with the drug Disulfiram (Antabuse) which would stop this gene from working and cause the Asian flush in non-Asians. PMC2659709 [http://www.ncbi.nlm.nih.gov/pmc/art...
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rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Disulfiram (...
1 snp
(hide) Asperger syndrome
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rs1322784, an intragenic SNP associated with the 'disrupted in schizophrenia' DISC1 gene, was reported to be associated with asperger's syndrome This same study also implicated the 'HEP3 haplotype' in asperger's syndrome. The HEP3 haplotype contains two SNPs in the DISC1 gene, rs751229 and rs3738401, and was first reported as a haplotype under-represented in individuals with affective disorders.
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In a study size of 117 Caucasians with Asperger syndrome and 426 controls 'Single nucleotide polymorphism rs6716901 in SLC25A12 gene is associated with Asperger syndrome' found association of this SNP's minor allele (A) in SLC25A12 gene with Asperger syndrome. Minor allele (A) was associated with OR 1.70 (0.98-3.02) P=0.008 after correcting for multiple testing. The study did not replicate previously reported associations with rs2056202 and rs3765166 which authors speculate could be due to differences in diagnosing AS and heterogenity of sample, though they admit to limitation of sample size and lack of replication sample.
2 snps
(hide) Asthma
Magnitude: 2
Frequency: 31.0%
Repute:Bad
References:2
Frequency: 31.0%
Repute:Bad
References:2
possible risk for allergic asthma
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A large study of Caucasian children has identified this SNP in the TBX21 gene (and one other, rs16947078) as defining a haplotype associated with increased risk for allergic asthma. The odds ratio associated with rs11650354(T;T) homozygotes compared to rs11650354(C;C) homozygotes for allergic asthma is reported to be 8.13 (CI: 2.5-26.9). Heterozygotes may be at slightly higher risk. Polymorphisms in inflammation-related genes are associated with susceptibility to major depression and antidepressant response.
1.6x increased prostate cancer risk
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This SNP is upstream of the IL10 gene, and is also known as the -1082G>A IL10 SNP. Dust mite exposure modifies the effect of functional IL10 polymorphisms on allergy and asthma exacerbations. Dust mite exposure significantly modified the relation between 3 SNPs in IL10 (rs1800896, rs3024492, and rs3024496). Homozygosity for the minor allele of each of the 3 SNPs was associated with increased risk of occurrence ( approximately 3-fold to 39-fold increase). A study of 258 prostate cancer cases concluded that the rs1800896(A) allele, known to result in lower levels of this anti-inflammatory cytokine, was positively associated with risk (AG vs. GG, odds ratio of 1.69, CI: 1.10-2.60; AA vs. GG, OR of 1.81, CI: 1.11-2.96).
Magnitude: 2
Frequency: 57.5%
Repute:Bad
References:0
Frequency: 57.5%
Repute:Bad
References:0
Normal (higher) risk of Asthma. This is normal for white people. But this (C;T) has 1.58x the risk compared to T;T (normal for non-white people). Tested in Koreans.
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Asthma
2.1x risk for Aspirin Induced Asthma. But possibly lower risk of intractible Grave's disease. Only tested in Japanese people. Might not be true for other races. May also be slightly protective against lupus (in Chinese people).
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rs4794067(C;C) and rs4794067(C;T) genotypes for the TBX21 gene are calculated to be at 2.15 fold higher risk (CI: 1.26-3.64) for aspirin-induced asthma (AIA) compared to rs4794067(T;T) homozygotes, based on a study of 72 patients vs 640 controls in a study of a Japanese population. Note that in this population, but perhaps not others, linkage disequilibrium exists between this SNP located upstream of the gene, rs4794067, and a common synonymous SNP located in the first exon, rs2074190, with a predictive accuracy of 92%. On the other hand, rs4794067(C;C) may greatly decrease the risk of lupus if rs17250932(C;C) is also present (at least in Chinese people). And those 2 SNPs also reduce the risk of intractable Graves' disease (at least in Japanese people).
Normal (higher) risk of Asthma.
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rs4950928 in CHI3L1 is likely to play roles in the predisposition to schizophrenia. An attempt to repeat the association between rs4950928 and risk for schizophrenia in an ethnically identical population (Japanese) as well as a new population (Han Chinese) failed to show any significant association. In contrast to previous studies, in this study of 6514 Danish adults the rs4950928(G) allele - rather than the (C) allele - was found to be associated with asthma. [PharmGKB:Non-Curated GWAS Results: Effect of Variation in CHI31 on Serum YKL-40 Level, Risk of Asthma, and Lung Function (Initial Sample Size: 632 individuals; Replication Sample Size: 206 children; Risk Allele: rs4950928-G). This variant is associated with YKL-40 levels.] [OMIM:CHITINASE 3-LIKE 1; CHI3L1] [GWAS:YKL-40 levels]
Normal risk for Childhood Asthma.
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rs7216389, a SNP in the ORMDL3 gene on chromosome 17q21, was associated with susceptibility to childhood asthma in a study of ~1,000 British patients. The variation appears to be linked to altered levels of the ORMDL3 mRNA, which was shown in a cohort study of ~5,000 British and German patients to be correlated to childhood asthma. A large study of Scottish asthma patients replicated these results, finding that a single copy of the T allele conferred an odds ratio of 1.50 (CI: 1.24-1.81) and 2 copies conferred an odds ratio of 2.11 (CI: 1.71-2.61), respectively. [PharmGKB:Non-Curated GWAS Results: Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma (Initial Sample Size: 994 cases, 1,243 controls; Replication Sample Size: 2,320 cases, 3,301 controls; Ri...
1.16x increased risk for asthma
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A study of ~170 families led to a slight association between rs2278206 and atopic asthma. The risk genotype - in dbSNP orientation, not as published - is rs2278206(T;T). Conversely, the rs2278206(C;C) genotype was rarely (odds ratio 0.13) seen in patients with atopic asthma.
respond better to steroids
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This SNP encodes a variation in the 33rd amino acid of the protein encoded by the TBX21 gene. Although 95% or so of all Caucasians carry two copies of the rs2240017(G) allele, as oriented in dbSNP orientation, and are thus rs2240017(G;G) homozygotes, a few individuals are rs2240017(C;G) heterozygotes. These heterozgotes are reported to improve better over time in response to corticosteroid treatment for asthma than the rs2240017(G;G) homozygotes. So far, studies have not linked, however, this SNP to any change in the overall risk of asthma itself. Although the effect observed was strong, in that treating rs2240017(C;G) heterozygotes ultimately (over 4 years) yields average airway responsiveness in the normal range (i.e. in the same range as for nonasthmatics), the authors point out that th...
somewhat increased risk for type-1 diabetes and allergic asthma
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rs3804100, also known as 1350T/C, is a SNP in the toll-like receptor 2 TLR2 gene. A study of 700 T1D children, 357 nuclear families with T1D children and 796 children from the 'Environment and Childhood Asthma' study concluded that both type-1 diabetes and allergic asthma were significantly associated with the rs3804100(T) allele.
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rs2070874 is a SNP in the promoter region of the interleukin 4 IL4 gene. This SNP is one of five SNPs reported to be useful in a SNP set defining the risk of dying from prostate cancer among patients with the disease; see gs242 and gs243. Visceral leishmaniasis (VL) caused by Leishmania chagasi is endemic to northeast Brazil. A positive delayed-type hypersensitivity skin test response (DTH+) is a marker for acquired resistance to disease. the DTH- phenotype was associated with SNP rs2070874 at IL4 (OR 3.14; P=0.006; 95% CI=1.38-7.14), and SNP rs30740 between LECT2 and TGFBI (OR 3.00; P=0.042; 95% CI=1.04-8.65)
1.8x risk
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rs2303067, a SNP in the SPINK5 gene, has been significantly associated with susceptibility to atopic dermatitis. The risk allele for rs2303067 is (A). rs2303067 has also been associated with predisposition to asthma, . From this study: 'A significant association between rs2303067 and the development of asthma was observed (OR 1.77; 95%CI: 1.02-3.06, P=0.041 for rs2303067(A;A) homozygotes). Atopic carriers of rs2303067 showed an increased risk for asthma and asthma symptoms (OR 2.06; 95%CI: 1.01-4.20, P=0.047). When children with a combination of asthma and atopic dermatitis were compared with normal controls, the rs2303067(A) genotype was more prevalent in the disease group (OR 4.56; 95%CI: 1.370-15.12, P=0.007).' [OMIM:?]
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
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'''rs6967330''', a SNP found to be associated with early childhood asthma characterized by severe exacerbations , is situated at chr7:105658451 in the CDHR3 gene coding region. The CDHR3 gene encodes a transmembrane protein that belongs to the cadherin family. Proteins in the cadherin family are involved in homologous cell adhesion and important for several cellular processes, including epithelial polarity, cell-cell interaction and differentiation, but the specific role of CDHR3 is unclear. The identification of rs6967330 in a genome-wide association study (GWAS) of asthma indicates that CDHR3 might be an asthma susceptibility locus. == Asthma and Genetics == Asthma is a common inflammatory disease of the airways characterized by symptoms of wheezing, chest tightness, and shortness of bre...
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associated with bronchodilator response among a sample of 209 children and their parents participating in the Childhood Asthma Management Program, the minor allele was associated with lower BDR compared to the homozygous major allele [PharmGKB:Curated This variant is associated with acute response to inhaled ? agonists in both childhood and adult asthmatic patients.]
2.2x risk for AIA
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rs2074190(G;G) and rs2074190(A;G) genotypes for the TBX21 gene are calculated to be at 2.19 fold higher risk (CI: 1.27-3.77) for aspirin-induced asthma (AIA) compared to rs2074190(A;A) homozygotes, based on a study of 72 patients vs 640 controls in a study of a Japanese population. Note that in this population, but perhaps not others, linkage disequilibrium exists between this SNP located in the first exon, rs2074190, and a SNP located upstream of the gene, rs4794067, with a predictive accuracy of 92%.
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asthma related influences sleep patterns [http://originsgenomeresources.net/musings/?p=62] [OMIM:ASTHMA SUSCEPTIBILITY 2]
normal
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
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pediatric asthma in a Taiwanese population. Prognostic significance of genetic variants in the IL-23/Th17 pathway for the outcome of T cell-depleted allogeneic stem cell transplantation.
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linked to asthma Carrying 1 or 2 copies of the minor allele of SNP rs1154404 was associated with decreased risk of asthma (relative risk [RR], 0.77; 95% CI, 0.61-0.97; P = .028 for 1 copy and RR, 0.66; 95% CI, 0.44-0.99; P = .046 for 2 copies). Homozygosity for the minor allele increased risk of asthma (RR, 1.60; 95% CI, 1.13-2.26; P = .0077). CLINICAL IMPLICATIONS: The association of GSNOR polymorphisms with asthma suggests a potential therapeutic target.
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news linked to asthma Asthma and genes encoding components of the vitamin D pathway. Genetic evidence for a role of IL33 in nasal polyposis. Interleukin-1 receptor-like 1 polymorphisms are associated with serum IL1RL1-a, eosinophils, and asthma in childhood. [PharmGKB:Curated GWAS results: Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction. (Initial Sample Size: 9,392 individuals; Replication Sample Size: 12,118 individuals); (Region: 2q12.1; Reported Gene(s): IL1RL1; Risk Allele: rs1420101-A); (p-value= 0.00000000000005).This variant is associated with Plasma eosinophil count.] [GWAS:Plasma eosinophil count]
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[GWAS:Asthma]
increased risk
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rs977785, a SNP purported to be in the promoter of the LY86 gene, is reported to be associated with mite-sensitive allergies in children, based on a study of 500+ Taiwanese patients. The allele that is underrepresented (and thus protective?) is the minor allele, which in dbSNP orientation is rs1334710(A).
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asthma phenotype in childhood OR=7.84, 95% CI=1.04-58.92, P=0.045 Gene-environment interaction effects on the development of immune responses in the 1st year of life. A meta-analysis of candidate gene polymorphisms and ischemic stroke in 6 study populations: association of lymphotoxin-alpha in nonhypertensive patients. Genetic risk factors in recurrent venous thromboembolism: A multilocus, population-based, prospective approach. Association of 77 polymorphisms in 52 candidate genes with blood pressure progression and incident hypertension: the Women's Genome Health Study. A candidate gene association study of 77 polymorphisms in migraine. The CC16 A38G polymorphism is associated with the development of asthma in children with allergic rhinitis. [GWAS:Chronic obstructive pulmonary disease-...
normal
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rs8069176 is one of several SNPs from a region on chromosome 17q21 that has been linked to risk for asthma. A total of 651 French patients with asthma, from among 1,621 subjects in 388 families, were analyzed for SNPs in the (17q21) region. An association was found between this SNP and early-onset asthma (but not with later onset asthma) which was significant after correction at p < 0.001. Upon further study, this association was seen primarily only in children exposed to tobacco smoke. The odds ratio was 2.9, based on the most likely assumption that this risk is associated only with the recessive homozygous state (and not the heterozygous state, which is still possible). [PharmGKB:Curated This variant in the 17q21 region was strongly associated (P<0.001) with early-onset asthma. Th...
normal
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rs2305480 is one of several SNPs from a region on chromosome 17q21 that has been linked to risk for asthma. A total of 651 French patients with asthma, from among 1,621 subjects in 388 families, were analyzed for SNPs in the (17q21) region. An association was found between this SNP and early-onset asthma (but not with later onset asthma) which was significant after correction at p < 0.001. Upon further study, this association was seen primarily only in children exposed to tobacco smoke. The odds ratio was 2.77, based on the most likely assumption that this risk is associated only with the recessive homozygous state (and not the heterozygous state, which is still possible). [PharmGKB:Curated This variant in the 17q21 region was strongly associated (P<0.001) with early-onset asthma. T...
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Dust mite exposure modifies the effect of functional IL10 polymorphisms on allergy and asthma exacerbations. Dust mite exposure significantly modified the relation between 3 SNPs in IL10 (rs1800896, rs3024492, and rs3024496). Homozygosity for the minor allele of each of the 3 SNPs was associated with increased risk of occurrence ( approximately 3-fold to 39-fold increase)
normal
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rs4795400 is one of several SNPs from a region on chromosome 17q21 that has been linked to risk for asthma. A total of 651 French patients with asthma, from among 1,621 subjects in 388 families, were analyzed for SNPs in the (17q21) region. An association was found between this SNP and early-onset asthma (but not with later onset asthma) which was significant after correction at p < 0.001. Upon further study, this association was seen primarily only in children exposed to tobacco smoke. The odds ratio was 2.5, based on the most likely assumption that this risk is associated only with the recessive homozygous state (and not the heterozygous state, which is still possible). [PharmGKB:Curated This variant in the 17q21 region was strongly associated (P<0.001) with early-onset asthma. Th...
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rs1978331 is one of several SNPs associated with asthma and allergy susceptibility based on a study of 341 Caucasian families. [OMIM:LEUKOTRIENE A4 HYDROLASE; LTA4H]
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rs8067378 is the strongest associating SNP from a region of chromosome 17q21 found in a large (ultimately over 7,000 patients in 3 populations) genome-wide association study of childhood asthma. Since the associated SNPs were also strongly associated (p < 10<sup>-22</sup>) in cis with transcript levels of from the ORMDL3 gene, the authors concluded that genetic variants regulating ORMDL3 expression are determinants of susceptibility to childhood asthma. Assessing the reproducibility of asthma candidate gene associations, using genome-wide data. Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene. Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in mexican children. Allele-specific chromatin remode...
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Higher lipoprotein-associated phospholipase predicts cardiovascular disease rs2033547 rs1051931 rs10520358 asthma related [OMIM:ASTHMA AND ATOPY, SUSCEPTIBILITY TO]
average
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rs1334710, a SNP purported to be in the promoter of the LY86 gene, is reported to be associated with mite-sensitive allergies in children, based on a study of 500+ Taiwanese patients. The allele that is underrepresented (and thus protective?) is the minor allele, which in dbSNP orientation is rs1334710(G).
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Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes. Double-strand break damage and associated DNA repair genes predispose smokers to gene methylation. [GWAS:Asthma]
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23andMe blog asthma
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subjects without T-allele in SNP rs320995 had 3.1 times higher risk of asthma (Pobserved=0.00004)
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rs2280089, a SNP in the ADAM33 gene, has been linked to a predisposition to asthma and bronchial hyperresponsiveness.
Frequency: 79.6%
References:7
References:7
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rs12422149 linked to asthma [PharmGKB:Curated In an 80-patient study, the A allele of this variant was associated with significantly reduced plasma concentrations of montelukast and with poor response to treatment with montelukast.]
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rs20541 is a C/T polymorphism on the interleukin 13 gene IL13 associated with IgE levels. rs20541 influences the effect of maternal smoking during pregnancy and persistent childhood asthma rs1295685 and rs20541 were significantly associated with elevated IgE levels in pooled analyses. rs2569190(T;T) and rs2569191(C;C) genotypes associated with lower IgE 23andMe blog psoriasis Europeans rs20541(G) 1.27x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 5q31.1; Reported Gene(s): IL13; Risk Allele: rs20541-G); (p-value= 0.000000000000005).This variant is associated with Psoriasis.] [OMIM:PSORIASIS SUSCEP...
References:0
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Genetic variation in GSNOR and childhood asthma. The name GSNOR is usually used in mice, for the human gene ADH1C but the paper provides the human snp rs28730619
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rs44707, a SNP in the ADAM33 gene, has been linked to a predisposition to asthma and bronchial hyperresponsiveness.
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Polymorphisms within the C3 gene are associated with specific IgE levels to common allergens and super-antigens among atopic dermatitis patients. [Association of the C3 gene polymorphisms with susceptibility to adult asthma].
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asthma rs6591255 variant allele is associated with increased risk of new-onset asthma upon exercise based on a study of 1,610 American children (hazard ratio 1.4, CI: 1.1-1.9)
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
normal
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rs9272346 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 5.49 (CI 4.83-6.24), and for homozygotes, 18.52 (CI 12.69-27.03). Note that the (A) allele is the most common in various human populations; instead of labeling (A) as a risk allele, we could consider the (G) allele protective. Risk alleles for multiple sclerosis identified by a genomewide study. Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. [PharmGKB:Curated GWAS ...
normal
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rs37973 is a SNP in the promoter region of the glucocorticoid induced transcript 1 GLCCI1 gene on chromosome 7. Based on 4 populations totaling 900+ asthma patients, the rs37973(G) allele was associated (p = 0.0007, pooled data) with lower amounts of improvement of lung function in response to inhaled glucocorticoids such as budesonide. The mean (±SE) increase in forced expiratory volume in 1 second (FEV1) in treated rs37973(G;G) patients was about one third of that seen in rs37973(A;A) patients (3.2±1.6% vs. 9.4±1.1%). Based on dividing the response into highest vs lowest quartiles of response, the allelic odds ratio of falling into the lowest responding quartile based on an additive genetic model was calculated to be 1.52 (CI: 1.13 - 2.03). Genotype accounted for about 7% ...
normal asthma risk in certain populations
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common...
normal/common in clinvar Found in 56% of all Caucasians on average, this genotype leads to a relative risk of 1.00, which is the most common risk, for late-onset (adult) asthma.
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rs1837253 is a SNP found a bit upstream of the thymic stromal lymphopoietin TSLP gene on chromosome 5. The TSLP protein plays a role in inflammation of cells in the trachea and alveoli therefore may have a causative role in certain types of asthma. The rs1837253(T) allele has been found to reduce the risk of developing late-onset (adult) asthma in several studies, and it is recognized by the CPMC Study as one they report to their participants. [GWAS:None]
normal but highest IgE levels
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rs2251746 is a SNP in the gene encoding the alpha chain of the high affinity receptor for IgE (FCER1A) on chromosome 1q23. High levels of serum IgE are associated with allergies, and are mediators of autoimmune diseases. An examination of over 11,000 Germans led to the conclusion that rs2251746 (and one other FCER1A SNP, the tightly linked rs2427837) were strongly associated with high levels of serum IgE. The more common (T) allele was associated with higher serum IgE, and the effect appeared to be additive. Therefore, homozygous rs2251746(C;C) individuals may be at lower risk for atopic eczema and asthma than carriers of one or two (T) alleles. In Japanese patients, rs2251746 may be a poor predictor, and the neighboring rs2427827 may be more appropriate. Common variants in FCER1A influenc...
common on affy axiom data http://www.diygenomics.org/webapp/gen_data.php
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Mentioned in retracted [GWAS:Asthma]
common in complete genomics
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asthma related [OMIM:ASTHMA AND ATOPY, SUSCEPTIBILITY TO]
normal
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rs569108, a SNP in the MS4A2 gene, has been linked in a Japanese population to a predisposition to childhood asthma, with an odds ratio of 3 . The risk allele in dbSNP orientation is (C). [Note: no (C;C) homozygotes were observed in this population.] Gene-environment interaction effects on the development of immune responses in the 1st year of life. Analysis of polymorphisms in 16 genes in type 1 diabetes that have been associated with other immune-mediated diseases. A meta-analysis of candidate gene polymorphisms and ischemic stroke in 6 study populations: association of lymphotoxin-alpha in nonhypertensive patients. Association of 77 polymorphisms in 52 candidate genes with blood pressure progression and incident hypertension: the Women's Genome Health Study. A candidate gene association...
normal
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rs4986790, a SNP also known as Asp299Gly (and also 896A/G) in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in th...
normal
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rs4986791, a SNP also known as Thr399Ile (and also 1196C/T) in the TLR4 gene, is often studied along with a cosegregating SNP known as Asp299Gly, rs4986790. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986791 is (T). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in t...
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asthma related This SNP is in the promoter region of the IL-13 gene PMID: 17615386 IL-13 is involved in pulmonary inflammation, remodeling and susceptibility to chronic obstructive pulmonary disease (COPD). This IL13 promoter polymorphism may modulate the adverse effects of cigarette smoking on pulmonary function in long-term cigarette smokers. Every 20 pack-year increment in smoking was associated with a 2.4% reduction in mean ppFEV1(forced expiratory volume in 1 second, a measure used to assess lung disease, like COPD) in the common homozygous (CC) or heterozygous (CT) promoter genotypes, and an 8.2% reduction in mean ppFEV1 in minor allele homozygotes (TT, recessive model). *pack-year= packs per day x years smoked rs1800925 and/or rs11568506 related to psoriasis and/or Crohn's disease ?...
common for Caucasians on the 23andme platform
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rs574174, a SNP in the ADAM33 gene, has been linked to a predisposition to asthma and bronchial hyperresponsiveness. Exo-proofreading, a versatile SNP scoring technology. Analysis of polymorphisms in 16 genes in type 1 diabetes that have been associated with other immune-mediated diseases. The role of polymorphisms in ADAM33, a disintegrin and metalloprotease 33, in childhood asthma and lung function in two German populations. ADAM33, a new candidate for psoriasis susceptibility. Adam33 polymorphisms are associated with COPD and lung function in long-term tobacco smokers.
54 snps
(hide) Atherosclerosis
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In 630 patients with essential hypertension (EHT) among males significant differences in rs5351 and rs5333 influencing atherosclerosis
1 snp
(hide) Atopic dermatitis
0.83x reduced risk of Atopic Dermatitis. This seems to be a proxy that 23andMe uses for the filaggrin gene variants that they can't measure directly.
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Atopic Dermatitis
Normal risk of Atopic Dermatitis.
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23andMe blog associated rs7927894(T) with Crohn’s disease 1.16x and atopic dermatitis [PharmGKB:Non-Curated GWAS results: A common variant on chromosome 11q13 is associated with Dermatitis, Atopic. (Initial Sample Size: 939 cases, 975 controls, 1,097 family members; Replication Sample Size: 2,637 cases, 3,957 controls); (Region: 11q13.5; Reported Gene(s): C11orf30; Risk Allele: rs7927894-A); (p-value= 0.0000000008).This variant is associated with Dermatitis, Atopic.] [OMIM:?] [GWAS:Atopic dermatitis]
Frequency: 9.2%
References:1
References:1
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[GWAS:Atopic dermatitis]
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[GWAS:Atopic dermatitis]
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rs2303064, a SNP in the SPINK5 gene, has been associated with susceptibility to atopic dermatitis.
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[GWAS:Atopic dermatitis]
1.8x risk
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rs2303067, a SNP in the SPINK5 gene, has been significantly associated with susceptibility to atopic dermatitis. The risk allele for rs2303067 is (A). rs2303067 has also been associated with predisposition to asthma, . From this study: 'A significant association between rs2303067 and the development of asthma was observed (OR 1.77; 95%CI: 1.02-3.06, P=0.041 for rs2303067(A;A) homozygotes). Atopic carriers of rs2303067 showed an increased risk for asthma and asthma symptoms (OR 2.06; 95%CI: 1.01-4.20, P=0.047). When children with a combination of asthma and atopic dermatitis were compared with normal controls, the rs2303067(A) genotype was more prevalent in the disease group (OR 4.56; 95%CI: 1.370-15.12, P=0.007).' [OMIM:?]
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[GWAS:Atopic dermatitis]
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[GWAS:Atopic dermatitis]
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[GWAS:Atopic dermatitis]
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[GWAS:Atopic dermatitis]
Frequency: 46.2%
References:1
References:1
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[GWAS:Atopic dermatitis]
Frequency: 62.8%
References:8
References:8
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[PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs13015714-C).] [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 8; CELIAC8] [GWAS:Atopic dermatitis] [GWAS:Celiac disease]
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[GWAS:Atopic dermatitis]
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[GWAS:Atopic dermatitis]
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[GWAS:Atopic dermatitis]
Frequency: 77.9%
References:3
References:3
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[GWAS:None]
Frequency: 82.3%
References:1
References:1
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[GWAS:Atopic dermatitis]
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[GWAS:Atopic dermatitis]
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[GWAS:Atopic dermatitis]
Frequency: 94.7%
References:1
References:1
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[GWAS:Atopic dermatitis]
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[GWAS:Atopic dermatitis]
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[GWAS:None]
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[GWAS:Atopic dermatitis]
24 snps
(hide) Atrial fibrillation
Lowest risk (13% of white women) of Atrial Fibrillation reported by 23andMe
The two atrial fibrillation SNPs mentioned by 23andMe are both normal. This causes the heart to form normally and gives the lowest risk of Atrial Fibrillation (quivering of the top part of the heart) that 23andMe reports. It also seems to lower the risk of Cardioembolic ischemic stroke (blocked blood flow to the brain) although 23andMe doesn't mention that. For European women, 23andMe reports this as a 13.0% risk, compared to the 15.9% average. The risk is higher for men. Based on many quality studies, and confirmed for Europeans and partly for Asians.
increased risk of hypertension
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rs699 is a SNP in the angiotensin AGT gene that encodes a functional change. In most published literature, the name for this SNP is M235T, or perhaps Met235Thr, however its amino acid 268 (not 235) that varies based on the numbering in todays databases. rs699 is also occasionally known as C4072T. In any case, the rs699(C) allele encodes the threonine variant, which is associated with higher plasma angiotensin levels, and ultimately higher blood pressure leading to increased risk for hypertension associated disorders. This association was first reported in 1992 , and many studies, though not all, have replicated these findings. rs699 is also (generally) reported to be in tight linkage with rs5051, a neighboring SNP in the promoter of the AGT gene. rs699(C) has also been implicated as a risk...
0.86x decreased risk of Atrial Fibrillation This is the normal version which makes the heart form properly and makes people less likely to get Atrial Fibrillation (quivering of the top chambers of the heart caused by chaotic electrical signals) and less likely to have an Ischemic Stroke (blocked blood flow to the brain). But also check the other SNP nearby (rs10033464) which slightly affects Atrial Fibrillation too. 23andMe gave this a 4 star confidence rating as it has been heavily studied. It has been confirmed in Europeans and Asians.
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Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x. The results derived from a study of 78 Italians with atrial fibrillation (AF) and atrial flutter (AFL) agree with previously reported findings from the Icelandic study (), which also found that the rs2200733(T) was associated with AF/AFL disease. In 1,661 Icelandic ischemic stroke samples and two large European replication sets combined, rs2200733 was associated with cardioembolic stroke (CES) (odds ratio 1.54, p = 8.05 x 10e-9). rs2200733 even showed association to ischemic stroke that was not classified as cardioembolic stroke. rs2200733 and rs1003...
Magnitude: 1.9
Frequency: 82.3%
Repute:Good
References:13
Frequency: 82.3%
Repute:Good
References:13
0.92x decreased risk of Atrial Fibrillation and cardioembolic stroke. This is the normal version which makes the heart form properly and makes people slightly less likely to get Atrial Fibrillation (quivering of the top chambers of the heart caused by chaotic electrical signals) and less likely to have a cardioembolic stroke (blocked blood flow to the brain). But also check the other SNP nearby (rs2200733) which affects Atrial Fibrillation even more. 23andMe gave this a 4 star confidence rating as it has been heavily studied. It has been confirmed in Europeans.
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Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x. In 1,661 Icelandic ischemic stroke samples and two large European replication sets combined, rs10033464 was associated with cardioembolic stroke (CES) (odds ratio 1.27, p = 6.1 x 10e-4). rs2200733 and rs10033464 are strongly associated with AF in four cohorts of European descent. Variation in the 4q25 chromosomal locus predicts atrial fibrillation after coronary artery bypass graft surgery. Chromosome 4q25 variants and atrial fibrillation recurrence after catheter ablation. Common variants in KCNN3 are associated with lone atrial fibrillation. Associ...
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[PharmGKB:Curated shortened QT interval]
Frequency: 15.0%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Framingham Heart Study 100K project: genome-wide associations for cardiovascular disease outcomes (Initial Sample Size: 1,341-1,345 individuals, depending on measure (Framingham); Replication Sample Size: NR). This variant is associated with Atrial fibrillation.] [GWAS:Atrial fibrillation]
normal risk
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rs5065, also known as T2238C, is a SNP in the atrial natriuretic precursor A NPPA gene. A large study has been conducted in which 42,418 hypertensive participants 55 or older were followed for several years while on one of four medications: a diuretic, a calcium antagonist, an angiotensin-converting enzyme inhibitor, or an alpha-blocker. The primary endpoint was either fatal heart disease or a heart attack. The blood pressure after six months of rs5065(G;G) patients (note: genotype is in dbSNP orientation, not as published) was lower if the patients were treated with diuretics compared to other medications, with smaller variation seen for (A;A) genotypes. The authors noted that none of the findings retained statistical significance after correction for multiple comparisons, but since the t...
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and 23andMe blog report rs7193343(T) *1.2x odds of atrial fibrillation *1.1x odds of ischemic stroke *1.2x increased odds for cardioembolic stroke but not significant among a Han Chinese population [OMIM:?]
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[PharmGKB:Curated Risk or phenotype-associated allele: minor allele . Phenotype: This variant is associated with lone atrial fibrillation. Study size: 1,335 cases; 12,844 referants. Study population/ethnicity: Cases-German AF Network, Heart and Vascular Health Study, the Cleveland Clinic and Massachusetts General Hospital. Significance metric(s): OR (for each additional minor allele) = 1.47, 95% CI = 1.39 -1.54, P = 1.61 x 10(-7) . Type of association: CO;GN] [OMIM:?] [GWAS:Atrial fibrillation]
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rs3903239 (1q23) is a SNP discovered 46kb upstream of the PRRX1 gene (1). Recent work has shown PRRX1 is a transcriptional co-activator that enhances the DNA affinity of serum response factor (2). This protein, in turn, regulates numerous growth and differentiation factors, including muscle creatine kinase (MCK) (2). MCK controls growth and development genes, specifically in developing mesodermal muscle such as the heart (2). PrrX1-/- mice are embryonic lethal and have a significantly altered neonatal phenotype including microcephaly, cleft palate, and hypoplastic processes of the mandible (3). Other studies have shown this gene is involved in lung vascular development and skeletogenesis (4). A meta-analysis GWA study correlated rs3903239 with atrial fibrillation (p = 9.1x10^-11, discovery...
Frequency: 47.8%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Framingham Heart Study 100K project: genome-wide associations for cardiovascular disease outcomes (Initial Sample Size: 1,341-1,345 individuals, depending on measure (Framingham); Replication Sample Size: NR). This variant is associated with Atrial fibrillation.] [GWAS:Atrial fibrillation]
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[PharmGKB:Curated Risk or phenotype-associated allele: G . Phenotype: This variant is associated with lone atrial fibrillation. Study size: 1,335 cases; 12,844 referants. Study population/ethnicity: Cases-German AF Network, Heart and Vascular Health Study, the Cleveland Clinic and Massachusetts General Hospital. Significance metric(s): OR (for each additional minor allele) = 2.03, 95% CI = 1.79 -2.30, P = 2.5 x 10(-28) . Type of association: CO;GN] [OMIM:?] [GWAS:Atrial fibrillation]
References:2
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[PharmGKB:Non-Curated GWAS results: Framingham Heart Study 100K project: genome-wide associations for cardiovascular disease outcomes (Initial Sample Size: 1,341-1,345 individuals, depending on measure (Framingham); Replication Sample Size: NR). This variant is associated with Atrial fibrillation.] [GWAS:Atrial fibrillation]
Magnitude: 0
Frequency: 46.9%
References:9
Frequency: 46.9%
References:9
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news atrial fibrillation rs13376333 in KCNN3, with an odds ratio (OR) of 1.5 per copy of rs13376333(T); CI: 1.40–1.64, p = 1.83 × 10e-21. spitoon [PharmGKB:Curated Risk or phenotype-associated allele: T . Phenotype: This variant is associated with lone atrial fibrillation. Study size: 1,335 cases; 12,844 referants. Study population/ethnicity: Cases-German AF Network, Heart and Vascular Health Study, the Cleveland Clinic and Massachusetts General Hospital. Significance metric(s): overall combined odds ratio = 1.52, 95% CI 1.40-1.64, P = 1.83 x 10(-21) . Type of association: CO;GN] [OMIM:?] [GWAS:Atrial fibrillation]
Magnitude: 0
Frequency: 78.8%
Repute:Good
References:2
Frequency: 78.8%
Repute:Good
References:2
Magnitude: 0
Frequency: 89.2%
Repute:Good
References:1
Frequency: 89.2%
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
1 genoset 18 snps
(hide) Attention deficit hyperactivity disorder
Normal (higher) risk of ADHD symptoms. This is one normal and one rare form of the CLOCK gene. In addition to possibly affecting evening preference, it has been linked to normal Attention Deficit Hyperactivity Disorder symptom scores.
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rs1801260, a SNP in the CLOCK gene known as 3111 T/C, has been reported to influence sleep and activity patterns in patients affected by bipolar depression. From this article's abstract: 'Compared to T/T homozygotes, carriers of the C allele had a similar degree of severity of depression, but showed higher activity levels in the evening, a delayed sleep onset (mean 79 min later), and a reduced amount of sleep during the night (mean 75 min less).' Allele frequencies of T3111C SNP of hClock were significantly different between schizophrenics and controls (chi(2) = 19.738, P < 0.05). Schizophrenics had a significantly higher frequency of the C allele compared with controls (OR = 2.613, 95% CI = 1.693-4.034). (Han Chinese population.) There was a strong, significant association (P < 0.00...
2x risk of severe alcohol withdrawal. Possible increased odds of ADHD. Alcoholics with this are twice as likely to have seizures during alcohol withdrawal.
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rs27072, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27048. The rs27072 polymorphism has been shown to be significantly associated with ADHD in clinical samples of Canadian children aged 6 to 16 [Feng et al., 2005] and the significant association was also reported by Ouellet-Morin et al. in a Canadian twin study, 2008 (Am. J. of Medical Genetics Part B, 147B:1442-1449 (2008). The interaction between the dopamine transporter gene and age at onset in relation to tobacco and alcohol use among 19-year-olds. Association of promoter variants of human dopamine transporter gene with schiz...
1.7x risk for developing restless legs syndrome Variants in MEIS1 rs2300478, BTBD9 rs9357271, and MAP2K5/SKOR1 rs1026732 confer a significant risk of RLS in a US population. Association studies of variants in MEIS1, BTBD9, and MAP2K5/SKOR1 with restless legs syndrome in a US population.
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rs2300478, a SNP located in the MEIS1 gene, has been linked to restless legs syndrome, a common sleep disorder, with an overall odds ratio of 1.78 (CI: 1.52-2.09) for the (G) risk allele . The association between this SNP and RLS has been replicated in three European populations, within family lines but not in sporadic cases . The highest association to restless legs syndrome is a haplotype consisting of the rs6710341(A) and rs12469063(G) alleles. This haplotype gives rise to an odds ratio of 2.75 (CI: 2.23-3.41) . Variants in MEIS1 rs2300478, BTBD9 rs9357271, and MAP2K5/SKOR1 rs1026732 confer a significant risk of RLS in a US population. In another study, rs2300478 was not associated with attention deficit hyperactivity disorder (ADHD). Association studies of variants in MEIS1, BTBD9, and...
Slightly increased risk of developing restless legs syndrome rs3923809 is a A/G variation on human chromosome 6. Associated with: Restless legs syndrome. This SNP, located in an intron of the BTBD9 gene, has a variant that is seen somewhat more frequently in individuals with restless legs syndrome. The risk allele is rs3923809(A); carriers of two such alleles, i.e. those with rs3923809(A;A) genotypes, are estimated to be 1.9 fold more likely to have restless legs syndrome than rs3923809(G;G) individuals. The authors of this study suggest that perhaps half of the cases of restless legs syndrome may involve the rs3923809 risk genotypes. Consistent with this finding, another report about rs3923809 links the (G) minor allele to a lower frequency of restless legs syndrome with an overall odds ...
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This SNP, located in an intron of the BTBD9 gene, has a variant that is seen somewhat more frequently in individuals with restless legs syndrome. The risk allele is rs3923809(A); carriers of two such alleles, i.e. those with rs3923809(A;A) genotypes, are estimated to be 1.9 fold more likely to have restless legs syndrome than rs3923809(G;G) individuals. The authors of this study suggest that perhaps half of the cases of restless legs syndrome may involve the rs3923809 risk genotypes. Consistent with this finding, another report about rs3923809 links the (G) minor allele to a lower frequency of restless legs syndrome with an overall odds ratio of 0.57 (CI: 0.48-0.68). Note that 70-80% of all individuals in European populations carry one or two copies of the (A) major allele, yet restless le...
0.69x risk risk of developing restless legs syndrome
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rs4489954, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.69 (CI: 0.69-0.82) for the (T) minor allele. [PharmGKB:Curated In replicated GWAS case-control studies of Caucasian(European and French-Canadian) familial and sporadic RLS, the G allele of rs4489954 was significantly associated with Restless Legs Syndrome.]
Magnitude: 1.5
Frequency: 50.0%
Repute:Good
References:6
Frequency: 50.0%
Repute:Good
References:6
0.71x risk for restless legs
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rs12593813, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.71 (CI: 0.60-0.83) for the (A) minor allele. Restless Legs Syndrome: Preliminary Research [PharmGKB:Curated GWAS Results: Genome-wide association study of restless legs syndrome identifies common variants in three genomic regions (Initial Sample Size: 401 cases, 1,644 controls; Replication Sample Size: 1,158 cases, 1,178 controls; Risk Allele: rs12593813-G).] [GWAS:None] [GWAS:Restless legs syndrome]
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[GWAS:Attention-deficit/hyperactivity disorder]
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Association between rs2799573 and psychiatric disorders was shown in a 2013 study by the Cross-Disorder Group of the Psychiatric Genomics Consortium . In this study, genome-wide SNP data consisting of 1,250,922 autosomal SNPs were analyzed to identify genetic variants associated with autism spectrum disorder, ADHD, bipolar disorder, major depressive disorder, and schizophrenia. 33,332 cases and 27,888 controls included both unrelated and family-based samples (trios). A multinomial logistic regression procedure was used to identify the best-fitting model of relations between genotype and phenotype. This SNP, on chromosome 10 in an intron of CACNB2, was one of four genome-wide significant signals associated with the five psychiatric disorders (p = 4.29 x 10-8). The risk allele T exhibited al...
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[GWAS:Attention-deficit/hyperactivity disorder]
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[PharmGKB:Non-Curated GWAS results: Does parental expressed emotion moderate genetic effects in ADHD? an exploration using a genome wide association scan. (Initial Sample Size: 909 trios; Replication Sample Size: NR); (Region: 11q21; Reported Gene(s): PIWIL4; Risk Allele: rs2212361-C); (p-value= 0.0000009).This variant is associated with Attention-deficit/hyperactivity disorder symptoms (interaction).] [GWAS:Attention-deficit/hyperactivity disorder symptoms (interaction)]
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 10p14; Reported Gene(s): A2BP1; Risk Allele: rs1291846-T); (p-value= 0.000009).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
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[GWAS:Attention-deficit/hyperactivity disorder]
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[GWAS:Hyperactive-impulsive symptoms]
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[GWAS:Attention deficit hyperactivity disorder (time to onset)]
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 13q12.2; Reported Gene(s): GSX1, PDX1; Risk Allele: rs9512900-C); (p-value= 0.000009).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
Frequency: 18.6%
References:1
References:1
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[GWAS:Attention deficit hyperactivity disorder]
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[GWAS:Attention-deficit/hyperactivity disorder]
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[GWAS:Attention deficit hyperactivity disorder]
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[GWAS:Attention deficit hyperactivity disorder]
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 21q21.1; Reported Gene(s): Intergenic; Risk Allele: rs2826340-T); (p-value= 0.000002).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
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rs806377(C) together with rs6454674(G) make up a haplotype associated (p=0.008) with higher risk of ADHD. In addition, the haplotype was more associated (p=0.03) with ADHD in males than in females with the risk haplotype. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. Evidence for association between polymorphisms in the cannabinoid receptor 1 (CNR1) gene and cannabis dependence. Interaction between two independent CNR1 variants increases risk for cocaine dependence in European Americans: a replication study in family-based sample and population-based sample. Candidate genes for cannabis use disorders: findings, challenges and directions. The association between cannabinoid receptor 1 gene (CNR1) and cannabis dependence symptoms in adolescent...
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[GWAS:Attention deficit hyperactivity disorder]
normal
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rs4570625, also known as G-703T, is a SNP in the tryptophan hydroxylase 2 TPH2 gene. This SNP has been linked to several psychiatric and/or behavioural phenomena, including: * rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder * rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission * rs4570625(G;G) homozygosity was a significant predictor of clinical placebo response, being associated with greater improvement in anxiety symptoms. g2b2mh is rs4570625(G;G) is a significant predictor of clinical placebo response? maybe not panic disorder with a possible gender-dependent effect Transmission disequilibrium of polymorphic variants in the tryptophan hydroxylase-2 gene in attention-deficit/hyperactivity disorder. Associa...
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[GWAS:Attention deficit hyperactivity disorder (time to onset)]
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[GWAS:Attention deficit hyperactivity disorder]
Frequency: 36.7%
References:1
References:1
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[GWAS:Inattentive symptoms]
Frequency: 37.2%
References:1
References:1
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[GWAS:Attention deficit hyperactivity disorder]
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 2q33.1; Reported Gene(s): FLJ39061, FZD7; Risk Allele: rs1521882-A); (p-value= 0.000008).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
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[PharmGKB:Non-Curated GWAS results: Does parental expressed emotion moderate genetic effects in ADHD? an exploration using a genome wide association scan. (Initial Sample Size: 909 trios; Replication Sample Size: NR); (Region: 13q12.3; Reported Gene(s): Intergenic; Risk Allele: rs1161463-C); (p-value= 0.000002).This variant is associated with Attention-deficit/hyperactivity disorder symptoms (interaction).] [GWAS:Attention-deficit/hyperactivity disorder symptoms (interaction)]
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[GWAS:Attention deficit hyperactivity disorder]
Frequency: 38.9%
References:1
References:1
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[GWAS:Inattentive symptoms]
Associated with ADHD
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SNPs nominally associated with schizophrenia (rs3787283, rs3746544) were the same as those previously demonstrated to be associated with ADHD but with the opposite alleles, allowing the intriguing hypothesis that genetic variation at SNAP25 may be differentially associated with both schizophrenia and ADHD When comparing pooled results of multiple ADHD studies, only rs3746544(A) was found to have a significant association (p=0.028) with slightly increased risk (OR 1.15 at 95%) of ADHD. Support for the MnlI polymorphism of SNAP25; a Korean ADHD case-control study. Investigation of variation in SNAP-25 and ADHD and relationship to co-morbid major depressive disorder. Biased paternal transmission of SNAP-25 risk alleles in attention-deficit hyperactivity disorder.
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[GWAS:Attention deficit hyperactivity disorder]
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[GWAS:Inattentive symptoms]
Frequency: 40.7%
References:1
References:1
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[GWAS:Inattentive symptoms]
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[GWAS:Attention-deficit/hyperactivity disorder]
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Detection of genetic association and a functional polymorphism of dynamin 1 gene with nicotine dependence in European and African Americans. [GWAS:Attention-deficit/hyperactivity disorder]
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[GWAS:Attention deficit hyperactivity disorder]
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[GWAS:Inattentive symptoms]
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[GWAS:Attention deficit hyperactivity disorder]
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Exploration of 19 serotoninergic candidate genes in adults and children with attention-deficit/hyperactivity disorder identifies association for 5HT2A, DDC and MAOB. C allele associated with ADHD in adults.
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G allele associated with better response to treatment of ADHD with atomoxetine.
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A allele associated with better response to treatment of ADHD with atomoxetine.
Frequency: 46.0%
References:1
References:1
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[GWAS:Attention-deficit/hyperactivity disorder]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 16q21; Reported Gene(s): Intergenic; Risk Allele: rs1381102-A); (p-value= 0.000006).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
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SNPs nominally associated with schizophrenia (rs3787283, rs3746544) were the same as those previously demonstrated to be associated with ADHD but with the opposite alleles, allowing the intriguing hypothesis that genetic variation at SNAP25 may be differentially associated with both schizophrenia and ADHD
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Molecular genetics of attention-deficit/hyperactivity disorder: an overview. Shared heritability of attention-deficit/hyperactivity disorder and autism spectrum disorder. [GWAS:Attention deficit hyperactivity disorder]
Frequency: 47.8%
References:1
References:1
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Molecular genetics of attention-deficit/hyperactivity disorder: an overview. [GWAS:Attention-deficit/hyperactivity disorder]
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Support for association between ADHD and two candidate genes: NET1 and DRD1.
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 8q22.3; Reported Gene(s): YWHAZ; Risk Allele: rs931812-C); (p-value= 0.000005).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
Frequency: 50.4%
References:1
References:1
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[GWAS:Attention deficit hyperactivity disorder (time to onset)]
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 1p35.2; Reported Gene(s): Intergenic; Risk Allele: rs2180233-C); (p-value= 0.000009).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 2p22.3; Reported Gene(s): Intergenic; Risk Allele: rs6733379-G); (p-value= 0.000004).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
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Exploration of 19 serotoninergic candidate genes in adults and children with attention-deficit/hyperactivity disorder identifies association for 5HT2A, DDC and MAOB. A allele associated with ADHD in adults and children.
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[GWAS:Attention deficit hyperactivity disorder (time to onset)]
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[GWAS:Hyperactive-impulsive symptoms]
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 1q23.1; Reported Gene(s): ETV3L, ETV3; Risk Allele: rs6427356-G); (p-value= 0.000008).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
Frequency: 57.4%
References:1
References:1
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[GWAS:Inattentive symptoms]
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[GWAS:Attention-deficit/hyperactivity disorder]
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Adult attention deficit hyperactivity disorder (ADHD) 143 high-risk male subjects . rs6332 showed a trend toward an association between the A-allele and increased scores
Frequency: 61.1%
References:1
References:1
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[GWAS:Hyperactive-impulsive symptoms]
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Molecular genetics of attention-deficit/hyperactivity disorder: an overview. Shared heritability of attention-deficit/hyperactivity disorder and autism spectrum disorder. [GWAS:Attention deficit hyperactivity disorder (time to onset)]
normal
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rs1611115 (C-1021T) is a SNP near the dopamine beta-hydroxylase (DBH) gene. per OMIM, the T allele is associated with lower DBH expression in plasma (16 of TT genotype had DBH activity of 4.1, 46 of CT genotype had DBH activity of 25.2, and 112 of CC genotype had DBH activity of 48.1 nmol/min/ml) Association tests related to affective disorders such as ADHD were performed using four independent samples, healthy volunteers (N = 387), patients with affective disorders (N = 182), adult attention deficit hyperactivity disorder (ADHD) patients (N = 407), and patients with personality disorders (N = 637). Personality disorder patients carrying the DBH TT genotype exhibited higher neuroticism and novelty seeking scores as compared to individuals with the (C;C) or (C;T) genotype. Analyses on the l...
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 11q24.2; Reported Gene(s): KIRREL3; Risk Allele: rs1557488-T); (p-value= 0.000005).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 15q26.2; Reported Gene(s): SPATA8; Risk Allele: rs4533251-T); (p-value= 0.000004).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
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[GWAS:Attention-deficit/hyperactivity disorder]
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[PharmGKB:Non-Curated GWAS results: Does parental expressed emotion moderate genetic effects in ADHD? an exploration using a genome wide association scan. (Initial Sample Size: 909 trios; Replication Sample Size: NR); (Region: 6p21.2; Reported Gene(s): KIF6; Risk Allele: rs4714261-T); (p-value= 0.000002).This variant is associated with Attention-deficit/hyperactivity disorder symptoms (interaction).] [GWAS:Attention-deficit/hyperactivity disorder symptoms (interaction)]
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[GWAS:Attention deficit hyperactivity disorder]
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[GWAS:Attention-deficit/hyperactivity disorder]
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[GWAS:Attention-deficit/hyperactivity disorder]
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[GWAS:Attention-deficit/hyperactivity disorder]
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[GWAS:Attention deficit hyperactivity disorder]
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[GWAS:Attention deficit hyperactivity disorder (time to onset)]
Frequency: 81.7%
References:2
References:2
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[GWAS:Inattentive symptoms]
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[GWAS:Hyperactive-impulsive symptoms]
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anxiety-related personality traits, ADHD, schizophrenia part of a three marker haplotype rs737865-rs4680-rs165599 epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes popular in pubmed is associated with bipolar disorder and influences prefrontal aspects of verbal memory in bipolar patients and healthy controls. [PharmGKB:Curated In a study of 78 African American and 65 white patients diagnosed with schizophrenia or schizoaffective disorder, this SNP in the COMT gene was found to have significant associations with response to risperidone over 2-12 weeks in both African-American and white patients.] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
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rs1800544 (C-1291G) is a SNP located in the promoter region of ADRA2A (adrenergic receptor alpha 2A). GG genotype carriers had significantly higher consumption of sweet food products (Estonian Children Personality Behavior and Health Study subset, n = 419) GG genotype carriers had significantly higher scores on an assessment of depression, and significantly lower scores on morality and orderliness compared to CC carriers. girls with CC and CG genotypes scored higher than boys with the same genotypes on an assessment of extraversion. boys with GG genotypes, however, scored higher than girls with GG genotypes. GG genotype assoc. w/ higher scores of inattention Food Preference [OMIM:ALPHA-2A-ADRENERGIC RECEPTOR; ADRA2A]
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[OMIM:SOLUTE CARRIER FAMILY 6 (NEUROTRANSMITTER TRANSPORTER, DOPAMINE),]
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 1q25.3; Reported Gene(s): RGL1, GLT25D2; Risk Allele: rs10797919-G); (p-value= 0.000009).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 14q12; Reported Gene(s): Intergenic; Risk Allele: rs1951082-T); (p-value= 0.000005).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
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[GWAS:Inattentive symptoms]
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[PharmGKB:Non-Curated GWAS results: Does parental expressed emotion moderate genetic effects in ADHD? an exploration using a genome wide association scan. (Initial Sample Size: 909 trios; Replication Sample Size: NR); (Region: 21q21.1; Reported Gene(s): Intergenic; Risk Allele: rs2825388-A); (p-value= 0.000008).This variant is associated with Attention-deficit/hyperactivity disorder symptoms (interaction).] [GWAS:Attention-deficit/hyperactivity disorder symptoms (interaction)]
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[GWAS:Attention-deficit/hyperactivity disorder]
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[GWAS:Hyperactive-impulsive symptoms]
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[GWAS:Attention-deficit/hyperactivity disorder]
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[GWAS:Attention-deficit/hyperactivity disorder]
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[GWAS:Attention-deficit/hyperactivity disorder]
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Shared heritability of attention-deficit/hyperactivity disorder and autism spectrum disorder. [PharmGKB:Non-Curated GWAS results: Does parental expressed emotion moderate genetic effects in ADHD? an exploration using a genome wide association scan. (Initial Sample Size: 909 trios; Replication Sample Size: NR); (Region: 14q24.3; Reported Gene(s): Intergenic; Risk Allele: rs2360997-C); (p-value= 0.000008).This variant is associated with Attention-deficit/hyperactivity disorder symptoms (interaction).] [GWAS:Attention-deficit/hyperactivity disorder symptoms (interaction)]
common
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rs9296249, a SNP located in the BTBD9 gene region, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.62 (CI: 0.52-0.75) for the (C) minor allele. [PharmGKB:Curated GWAS Results: Genome-wide association study of restless legs syndrome identifies common variants in three genomic regions (Initial Sample Size: 401 cases, 1,644 controls; Replication Sample Size: 1,158 cases, 1,178 controls; Risk Allele: rs9296249-T).] [OMIM:RESTLESS LEGS SYNDROME, SUSCEPTIBILITY TO, 6] [GWAS:Restless legs syndrome]
common/normal Val/val (normal) variant of the Val66Met snp in the BDNF gene that codes for brain-derived neurotrophic factor. Met/met is associated with susceptibility to neuropsychiatric disorders.
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
Magnitude: 0
Frequency: 68.1%
Repute:Good
References:1
Frequency: 68.1%
Repute:Good
References:1
common in complete genomics
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G allele associated with better response to treatment of ADHD with atomoxetine.
Magnitude: 0
Frequency: 69.2%
Repute:Good
References:1
Frequency: 69.2%
Repute:Good
References:1
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 12q21.2; Reported Gene(s): PAWR; Risk Allele: rs7297018-A); (p-value= 0.000004).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
common on affy axiom data
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[GWAS:Attention deficit hyperactivity disorder (time to onset)]
Magnitude: 0
Frequency: 75.0%
Repute:Good
References:1
Frequency: 75.0%
Repute:Good
References:1
Magnitude: 0
Frequency: 77.0%
References:3
Frequency: 77.0%
References:3
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The G allele of rs10831284 is associated with a higher risk of attention deficit hyperactivity disorder (ADHD) and conduct disorder. [PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 4q13.3; Reported Gene(s): AMOTL1, CWC15, JMJD2D; Risk Allele: rs10831284-G); (p-value= 0.000002).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
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[GWAS:Attention deficit hyperactivity disorder]
Magnitude: 0
Frequency: 80.0%
Repute:Good
References:1
Frequency: 80.0%
Repute:Good
References:1
common on affy axiom data
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[GWAS:Attention deficit hyperactivity disorder (time to onset)]
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 12q15; Reported Gene(s): C12orf28; Risk Allele: rs789560-G); (p-value= 0.000007).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
normal risk of ADHD
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T allele may be associated with Attention deficit hyperactivity disorder.
common in complete genomics
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T allele associated with better response to treatment of ADHD with atomoxetine.
Magnitude: 0
Frequency: 86.7%
Repute:Good
References:3
Frequency: 86.7%
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Non-Curated Genome-wide association study of response to methylphenidate in 187 children with attention-deficit/hyperactivity disorder. (Initial Sample Size: 187 children; Replication Sample Size: NR); (Region: 5p15.31; Reported Gene: Intergenic; Risk Allele: rs11134178-T) This variant is associated with Attention-deficit/hyperactivity disorder.] [GWAS:Attention-deficit/hyperactivity disorder]
common on affy axiom data
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Associated with Attention deficit hyperactivity disorder. [PharmGKB:Non-Curated Genome-wide association study of response to methylphenidate in 187 children with attention-deficit/hyperactivity disorder. (Initial Sample Size: 187 children; Replication Sample Size: NR); (Region: 22q13.31; Reported Gene: Intergenic; Risk Allele: rs9627183-C) This variant is associated with Attention-deficit/hyperactivity disorder.] [GWAS:Attention-deficit/hyperactivity disorder]
Magnitude: 0
Frequency: 98.5%
Repute:Good
References:2
Frequency: 98.5%
Repute:Good
References:2
common in complete genomics
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The data were consistent for rs11568324, suggesting the existence of a rare allele conferring protection for ADHD
common for Caucasians on the 23andme platform
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rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission paper Association with and bipolar disorder in a Northern Swedish, Isolated Population. 182 patients and 364 unrelated control individuals. P = .001 rs11178997 significantly reduced TPH2 transcriptional activity by 22% and 7% in cell lines might have implications for the development and function of the serotonergic system in the brain. paper Carriers of the A-Allele of rs11178997 showed a decreased cortisol and ACTH stimulation. might be crucial factors for major depression pdf paper associated with bipolar disorder Minor allele yielded odds ratio of 1.5 (CI:1.2-1.9) for increased risk for bipolar disorder in a study of 883 Russian patients. Transmission disequilibrium of polymorphic variants in the tryp...
114 snps
(hide) Autism
Reduced Autism risk
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23andMe blog rs4307059 — compared to two copies of a C, each copy of the more common T version increased the odds of autism by 1.19 times. [http://dx.doi.org/10.1038/nature07999] [PharmGKB:Curated This SNP on 5p14.1 was associated with autism spectrum disorder in a combined analysis of four GWAS data sets with a total of more than 10,000 subjects of European ancestry. This SNP is in an intergenic region between CDH10 and CDH9 that contains several highly conserved genomic elements.] [OMIM:?]
slightly increased risk for autism
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A common SNP in the CNTNAP2 gene, rs7794745, is associated with increased risk for autism based on a study of 148 affected children from families with two more autistic children. Related article A genome-wide association study of autism reveals a common novel risk locus at 5p14.1. Do candidate genes discriminate patients with an autism spectrum disorder from those with attention deficit/hyperactivity disorder and is there an effect of lifetime substance use disorders? A common genetic variant in the neurexin superfamily member CNTNAP2 is associated with increased risk for selective mutism and social anxiety-related traits. Genetic variation in CNTNAP2 alters brain function during linguistic processing in healthy individuals. [PharmGKB:Curated This common variant in CNTNAP2 is significantl...
lower risk of autism
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Examination of tetrahydrobiopterin pathway genes in autism. Examination of association to autism of common genetic variation in genes related to dopamine.
2x risk of autism The C allele appears to increase risk of autism by an odds ratio of perhaps 1.8x
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rs1858830, located in promoter of the MET gene, has been linked to a 2x increase in the risk of autism based on a study of ~700 families. From OMIM 164860: 'In case-control analysis, the relative risk for autism was 2.27 for the CC genotype and 1.67 for the GC genotype compared to the GG genotype.' The association of rs1858830 in the MET gene with autism failed to replicate in 325 multiplex families and 10 trios of the International Molecular Genetic Study of Autism Consortium (IMGSAC), although another MET SNP did associate with autism (rs38845) Disruption of cerebral cortex MET signaling in autism spectrum disorder. Distinct genetic risk based on association of MET in families with co-occurring autism and gastrointestinal conditions. Association of genetic variation in the MET proto-onco...
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[OMIM:AUTISM, SUSCEPTIBILITY TO, 13; AUTS13]
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
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rs1322784, an intragenic SNP associated with the 'disrupted in schizophrenia' DISC1 gene, was reported to be associated with asperger's syndrome This same study also implicated the 'HEP3 haplotype' in asperger's syndrome. The HEP3 haplotype contains two SNPs in the DISC1 gene, rs751229 and rs3738401, and was first reported as a haplotype under-represented in individuals with affective disorders.
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*rs1445442 *rs2421826 *rs1358054 *rs722628 *rs536861
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[GWAS:Autism]
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[GWAS:Autism]
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rs6590109 has been reported to be a SNP potentially associated with increased risk for autism
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Based on a study of 170 patients with autism, this SNP (rs2300045) in the NRCAM gene and a haplotype containing it were associated with increased risk (p=0.0009 uncorrected, p=0.017 corrected).
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rs38845 is a SNP in the first intron of the transmembrane receptor tyrosine kinase of the hepatocyte growth factor/scatter factor MET gene. rs38845 is associated with autism (p < 0.004) in a study of 325 multiplex International Molecular Genetic Study of Autism Consortium (IMGSAC) families and 10 trios
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rs7925879 has been reported to be a SNP potentially associated with increased risk for autism
Frequency: 45.1%
References:0
References:0
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23andMe blog each copy of an G at rs12603112 increases the odds of autism in boys by 2.2x, although the G is very common
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Autism *rs1445442 *rs2421826 *rs1358054 *rs722628 *rs536861
None
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rs2710102, a common SNP in the CNTNAP2 gene, was found to be significantly associated (p<0.028) with a delayed onset of speech, as measured by the age at which a child speaks their first words, in children with autism. This effect is primarily seen in males, perhaps correlated with the 4-5x overrepresentation of males with autism compared with females. The confirmatory Stage 2 study was performed on 304 independent parent-child trios. However, the risk allele and the degree to which speech is delayed per genotype is unclear as published and awaits clarification by the authors. Speech development rs4431523, rs17236239 and significant associations (with P values from 0.01 to 5.0x10–5) between nonsense-word repetition and nine intronic SNPs (rs851715, rs10246256, rs2710102, rs759178,...
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rs3802905 has been reported to be a SNP potentially associated with increased risk for autism
normal autism risk
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rs6807362 is a SNP in the 5-hydroxytryptamine (serotonin) receptor 3, family member C HTR3C gene. In a study of 97 familes with at least one individual with autism, rs6807362 was significantly associated with the disorder (p = 0.0012).
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Haplotype rs12740310*C-rs3737296*G-rs12410279*A was overtransmitted (p(corrected)=0.0016), with a relative risk for autism of 1.8 in homozygous carriers [OMIM:MAP/MICROTUBULE AFFINITY-REGULATING KINASE 1; MARK1]
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Implicated as part of a haplotype of the dopamine D1 receptor DRD1 gene associated with autism spectrum disorders in families having only affected males. The haplotype is rs265981(C)-rs4532(A)-rs686(T) as published, though not necessarily as oriented in dbSNP.
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Implicated as part of a haplotype of the dopamine D1 receptor DRD1 gene associated with autism spectrum disorders in families having only affected males. The haplotype is rs265981(C)-rs4532(A)-rs686(T) as published, though not necessarily as oriented in dbSNP. [OMIM:DOPAMINE RECEPTOR D1; DRD1]
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Implicated as part of a haplotype of the dopamine D1 receptor DRD1 gene associated with autism spectrum disorders in families having only affected males. The haplotype is rs265981(C)-rs4532(A)-rs686(T) as published, though not necessarily as oriented in dbSNP. Significant association of DRD1 with nicotine dependence. A haplotype of the DRD1 gene is associated with alcohol dependence. The influence of serotonin- and other genes on impulsive behavioral aggression and cognitive impulsivity in children with attention-deficit/hyperactivity disorder (ADHD): Findings from a family-based association test (FBAT) analysis. Differential allelic expression of dopamine D1 receptor gene (DRD1) is modulated by microRNA miR-504. Heroin addiction in African Americans: a hypothesis-driven association study....
Possibly more 'Insistence on Sameness' on ADI-R test.Possibly increased FTND nicotine dependence.[http://www.ncbi.nlm.nih.gov/pubmed/22309839?dopt=Abstract
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rs167771 was significantly associated with autism spectrum disorder in a study of 144 patients. G allele associated with increased extra-pyramidal symptom risk as a result of risperidone treatment in a study of 321 psychiatric inpatients (81 presenting with EPS and 189 without) [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: The G variant of rs167771 was associated with increased risk for extrapyramidal symptoms in psychiatric patients receiving risperidone. Study size: 132. Study population/ethnicity: Patients with Schizophrenia or Bipolar disorder receiving antipsychotics; Caucasians; Spain; Catalonia. Significance metric(s): OR = 3.3; p = 0.00013. Type of association: PD.]
normal risk of autism
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Investigation of autism and GABA receptor subunit genes in multiple ethnic groups.
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Individuals homozygous or heterozygous for the rs11959298(A)-rs6596189(C) haplotype risk allele were 2.54 and 1.59 fold more likely to have autism, respectively, compared to rs11959298(G)-rs6596189(T) carriers. Note/caveat emptor: ~90% of the world's population carries what the authors from this for-profit genetic testing company call the 'risk haplotype', yet the frequency of autism is less than 1% (perhaps 1 in 150).
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[GWAS:Autism]
Frequency: 82.8%
References:0
References:0
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Individuals homozygous or heterozygous for the rs11959298(A)-rs6596189(C) haplotype risk allele were 2.54 and 1.59 fold more likely to have autism, respectively, compared to rs11959298(G)-rs6596189(T) carriers. Note/caveat emptor: ~90% of the world's population carries what the authors from this for-profit genetic testing company call the 'risk haplotype', yet the frequency of autism is less than 1% (perhaps 1 in 150).
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[GWAS:Autism]
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23andMe blog Wach copy of the A version of rs2217262 in the DOCK4 gene increased the odds of autism by 2.28 times. Note that almost 90% of people with European ancestry have two copies of the A version of this SNP, meaning that these results really mean that the rare C version of the SNP is protective against autism.
1.3x increased autism risk
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rs1143674 is a SNP in the integrin alpha-4 ITGA4 gene on chromosome 2. Across two sets of family samples (Irish and American), rs1143674 showed a slight association with increased risk for autism, with an odds ratio of 1.3 (p = 0.008).
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973 in en2, the C allele of rs1811399 in npas2, and the C allele of rs1234747 may contribute to autism by affecting microRNA rs1861972(A) + rs1861973(C) haplotype assoc. with '''protective''' effect against autism in a study of 818 Han Chinese (184 diag. autistics, 225 unrelated volunteers, 409 randomly selected) [OMIM:ENGRAILED 2; EN2]
Magnitude: 0.1
Frequency: 92.0%
Repute:Bad
References:4
Frequency: 92.0%
Repute:Bad
References:4
normal risk of Autism Like almost everyone else, you have the normal version of this SNP. Unfortunately you didn't get the rare alternative mutations that would halve your risk of autism. Your normal version (T;T) seems to reduce the expression of SEMA5A in the brains of people with autism.
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rs10513025 is a SNP located in chromosomal region 5p15, in between the SEMA5A and TAS2R1 genes. Based on a linkage and association mapping study of 1,031 multiplex autism families, rs10513025 was found to be associated with autism, and the expression of SEMA5A was seen to be reduced in brains from autistic patients. Although this finding was replicated, the authors caution that this SNP explains a very small fraction of the heritability of a complex disorder like autism, presumably due to their finding that the most common allele (present at a frequency of ~96%) is the allele associated with higher risk. The much rarer allele, rs10513025(C), is associated with a 0.55x reduced risk for autism (p=9.6x10e-6). [OMIM:?] [GWAS:Autism]
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973, the C allele of rs1811399, and the C allele of rs1234747 may contribute to autism by affecting microRNA rs1861972(A) + rs1861973(C) haplotype assoc. with '''protective''' effect against autism in a study of 818 Han Chinese (184 diag. autistics, 225 unrelated volunteers, 409 randomly selected) [OMIM:ENGRAILED 2; EN2]
normal
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A study of 151 Korean families reported that the rs2745557(A) allele of the PTGS2 gene, also known as cyclooxygenase-2 (Cox-2), was overtransmitted (p<0.01) in autism spectrum disorders.
Magnitude: 0
Frequency: 82.1%
Repute:Good
References:3
Frequency: 82.1%
Repute:Good
References:3
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Haplotype rs12740310*C-rs3737296*G-rs12410279*A was overtransmitted (p(corrected)=0.0016), with a relative risk for autism of 1.8 in homozygous carriers [OMIM:MAP/MICROTUBULE AFFINITY-REGULATING KINASE 1; MARK1]
common in complete genomics
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rs1804197, a SNP in the adenomatous polyposis of the colon APC gene, is associated with autism . Although many SNPs have been found in this gene in association with (successful) hunts for mutations predisposing individuals to colon cancers, this previously unidentified SNP is located in the 3' untranslated portion of the gene. Also in conjunction with a common four-SNP haplotype (TGAG for rs2229992, rs42427, rs459552, and rs465899), this SNP is reported to be associated with Asperger's sydrome in the Swedish population studied. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
41 snps
(hide) Autoimmune disease
HLA-DRB1*1501 carrier; higher multiple sclerosis risk Rs3135391(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.
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rs3135391 is highly correlated with the HLA-DRB1*1501 allele. The risk allele (T), is associated with a 3 to 6 fold higher risk for developing multiple sclerosis, and is the most significantly associated risk factor for MS. [PMC2892470] In one study, for example, the odds ratio was reported to be 3.04 (p < 1 x 10e-78). The HLA-DRB1*1501 allele has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and possibly narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. [PMC2892470] An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis would be to ensure...
3x higher risk of multiple sclerosis Rs3135388(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.
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rs3135388(T) is highly (> 99%) correlated with the HLA-DRB1*1501 allele; the risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. The risk per allele (or per haplotype) appears additive. It has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and, when linked with DQB1*0602, narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. Note: most publications refer to the risk allele as rs3135388(A), but in dbSNP and SNPedia orientation, it is rs3135388(T). An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis ...
2 snps
(hide) Autosomal Recessive Spastic Ataxia of Charlevoix-Saguenay
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Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a neurodegenerative disorder first described in French-Canadian individuals from the Charlevoix and Saguenay-Lac-St-Jean regions of northeastern Quebec. Symptoms begin in early childhood and typically involve muscle overactivity and lack of muscle coordination, resulting in difficulty walking, moving the limbs, and speaking. https://www.23andme.com/you/journal/arsacs/overview/ rs281865117
1 snp
(hide) Baldness
7x risk of baldness
7x risk of baldness according to an article in Nature. That site may require paid access; the abstract at is accessible.
Increased risk of Male Pattern Baldness. One copy of the risk allele, and one copy of the normal allele. Verified in Europeans and Asians. Family Tree DNA, which tends to skew heterozygous results like this in the most positive light, reports this as less likely to go bald, but 23andMe doesn't mention it.
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spitoon rs2180439(T;T) have 2x increased odds of male pattern baldness. [PharmGKB:Non-Curated Susceptibility variants for male-pattern baldness on chromosome 20p11. (Initial Sample Size: 296 cases, 347 controls; Replication Sample Size: 319 cases, 234 controls); (Region: 20p11.22; Reported Gene: PAX1, BQ013595, BE789145; Risk Allele: rs2180439-C) This variant is associated with Male-pattern baldness.] [OMIM:ALOPECIA, ANDROGENETIC, 3; AGA3] [GWAS:Male-pattern baldness]
1.6x increased risk of Male Pattern Baldness.
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nature Baldness OR = 1.60, P = 1.1 times 10-14). see also gs122 The risk allele is assumed to be rs1160312(A). Note that a haplotype consisting of rs201571(T) - rs6036025(G) has a perfect correlation (r2 = 1) with rs1160312(A), at least in the Caucasian population studied. [PharmGKB:Non-Curated Male-pattern baldness susceptibility locus at 20p11. (Initial Sample Size: 578 cases, 547 controls; Replication Sample Size: 1,351 cases, 2,485 controls); (Region: 20p11.22; Reported Gene: PAX1; Risk Allele: rs1160312-A) This variant is associated with Male-pattern baldness.] [OMIM:ALOPECIA, ANDROGENETIC, 3; AGA3] [GWAS:Male-pattern baldness]
increased risk of baldness slightly higher risk of baldness
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rs1385699, also known as Arg57Lys, is a SNP in the ectodysplasin A2 receptor EDAR2 gene. This gene is located on the X chromosome. The rs1385699(T) allele, which is the most common in European populations, was found to be associated with androgenetic alopecia in a case-control study of 400 males.
Normal (higher) risk of Male Pattern Baldness. Discovered by 23andWe based on customer surveys, and considered preliminary research.
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This is the 23andWe discovery: 'Male Pattern Baldness: Preliminary Research'. It affects appearance.
Normal (higher) risk of Male Pattern Baldness. Discovered by 23andWe based on customer surveys, and considered preliminary research.
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This is the 23andWe discovery: 'Male Pattern Baldness: Preliminary Research'. It affects appearance.
more likely to go bald before age 40 more likely to go bald before age 40
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male-pattern baldness. Full text available. *G less likely to go bald before age 40 *A more likely to go bald before age 40
increased risk of baldness more likely to go bald
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when used as part of gs122 this snp can influence male pattern baldness. Initial Sample Size: 578 cases, 547 controls Replication Sample Size: 1,351 cases, 2,485 controls Alopecia is readable, while the nature article is behind a paywall. This is one of the snps in gs122 Male Pattern Baldness [PharmGKB:Non-Curated GWAS results: Male-pattern baldness susceptibility locus at 20p11. (Initial Sample Size: 578 cases, 547 controls; Replication Sample Size: 1,351 cases, 2,485 controls); (Region: Xq12; Reported Gene(s): AR; Risk Allele: rs6625163-A); (p-value= 0.00000000005).This variant is associated with Male-pattern baldness.] [GWAS:Male-pattern baldness]
more likely to go bald more likely to go bald
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Along with rs201571 serves as a proxy for rs1160312. related to baldness
more likely to go bald; common
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23andMe seems to consider each A at rs925391 to have lowered men's odds of baldness by 11x. baldness *lowest P value of 2.1×10-12 for rs10521339 *family based rs938059 shows the lowest P value (4.03×10-6) (table 3) *rs6152 (P=6.66×10-10)
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Baldness paper from 23andMe June 2012 [GWAS:None]
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Baldness paper from 23andMe June 2012 [GWAS:None]
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rs6113491 linked to baldness by Male Pattern Baldness
Frequency: 52.2%
References:0
References:0
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Baldness paper from 23andMe June 2012
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Along with rs6036025 serves as a proxy for rs1160312. related to baldness [OMIM:ALOPECIA, ANDROGENETIC, 3; AGA3]
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baldness *lowest P value of 2.1×10-12 for rs10521339 *family based rs938059 shows the lowest P value (4.03×10-6) (table 3) *rs6152 (P=6.66×10-10)
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Baldness paper from 23andMe June 2012
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baldness *lowest P value of 2.1×10-12 for rs10521339 *family based rs938059 shows the lowest P value (4.03×10-6) (table 3) *rs6152 (P=6.66×10-10)
1 genoset 18 snps
(hide) Bardet-Biedl syndrome
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in clinvar
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Identification of a novel Bardet-Biedl syndrome protein, BBS7, that shares structural features with BBS1 and BBS2. Genetic interaction of BBS1 mutations with alleles at other BBS loci can result in non-Mendelian Bardet-Biedl syndrome. [OMIM:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in complete genomics common for Caucasians on the 23andme platform
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Bardet-Biedl syndrome is a genetic disease associated with a constellation of abnormalities including obesity, pigmentary retinopathy, polydactyly, renal abnormalities, learning disabilities, and hypogenitalism. [OMIM:BARDET-BIEDL SYNDROME 1]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
4 snps
(hide) Basal Cell Carcinoma
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23andMe blog rs2151280 G 1.19 Basal Cell Carcinoma [OMIM:?] [GWAS:Basal cell carcinoma]
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23andMe blog rs157935 T 1.23 Basal Cell Carcinoma parental imprinting effect [OMIM:?] [GWAS:Basal cell carcinoma]
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:3
Frequency: 85.0%
Repute:Good
References:3
common on affy axiom data
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23andMe blog rs11170164 T 1.35 Basal Cell Carcinoma [OMIM:?] [GWAS:Basal cell carcinoma]
3 snps
(hide) Basal cell carcinoma
0.78x decreased Basal Cell Carcinoma risk.
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
Normal risk of Basal Cell Carcinoma. Normal risk for this kind of skin cancer.
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
Magnitude: 1.5
Frequency: 28.3%
Repute:Bad
References:3
Frequency: 28.3%
Repute:Bad
References:3
Slightly higher risk for basal cell carcinoma
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rs12210050 was found to be associated with basal cell carcinoma based on a study by the eMERGE network in which electronic medical records were searched to find clinical associations associated with selected SNPs. [GWAS:Tanning]
~1.2x increased risk for several types of cancer
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rs401681 is a SNP in the CLPTM1-like CLPTM1 gene. The following studies span several types of cancer, and over 30,000 cases and 45,000 controls. deCODE press release reports rs401681 linked to basal cell carcinoma and many cancers for individuals with shorter telomeres, whereas those with long telomeres are at greater risk of melanoma. Neighboring rs2736098 also increases risk of cancer by affecting telomerase reverse transcriptase. The risk of these different cancers conferred by these two SNPs appears to be independent. 23andMe blog rs2736098 and rs401681 linked to many cancers, including susceptibility to pancreatic cancer However, a very large study (encompassing thousands of cases and controls) found no association between rs401681 and either (1) mean telomere length, or, (2) breast c...
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23andMe blog rs2151280 G 1.19 Basal Cell Carcinoma [OMIM:?] [GWAS:Basal cell carcinoma]
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23andMe blog rs157935 T 1.23 Basal Cell Carcinoma parental imprinting effect [OMIM:?] [GWAS:Basal cell carcinoma]
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:3
Frequency: 85.0%
Repute:Good
References:3
common on affy axiom data
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23andMe blog rs11170164 T 1.35 Basal Cell Carcinoma [OMIM:?] [GWAS:Basal cell carcinoma]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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rs78378222[C] (odds ratio (OR) = 2.36, P = 5.2 × 10?17). rs78378222 is in the 3? untranslated region of TP53 and changes the AATAAA polyadenylation signal to AATACA, resulting in impaired 3?-end processing of TP53 mRNA. Investigation of other tumor types identified associations of this SNP with prostate cancer (OR = 1.44, P = 2.4 × 10?6), glioma (OR = 2.35, P = 1.0 × 10?5) and colorectal adenoma (OR = 1.39, P = 1.6 × 10?4). However, we observed no effect for breast cancer, a common Li-Fraumeni syndrome tumor (OR = 1.06, P = 0.57, 95% confidence interval 0.88–1.27). [GWAS:Basal cell carcinoma]
8 snps
(hide) Behçet's disease
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This SNP is part of a haplotype reported for the KLRK1 gene, potentially associated with risk for colorectal cancer; see details at rs1049174. [GWAS:Behcet's disease]
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[GWAS:Behcet's disease]
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[GWAS:Behcet's disease]
1.2x higher risk for spondylitis
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rs1495965 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 1.2 (p=6.6x10e-6). 23andMe reports that the CC genotype at rs1495965 is associated with 1.56x higher odds of Behçet's disease, and the TT genotype with 0.64x lower odds, than the CT genotype. rs11209032 and rs1495965 no significant association with systemic sclerosis A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Investigation of the IL23R gene in a Spanish rheumatoid arthritis cohort. rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and OCTN1/2 variants. CARD15 and IL23R influences Croh...
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[GWAS:Behcet's disease]
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Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Polymorphisms in the genes encoding chemokine receptor 5, interleukin-10, and monocyte chemoattractant protein 1 contribute to cytomegalovirus reactivation and disease after allogeneic stem cell transplantation. Raised interleukin-10 is an indicator of poor outcome and enhanced systemic inflammation in patients with acute coronary syndrome. Analysis of eight genes modulating interferon gamma and human genetic susceptibility to tuberculosis: a case-control association study. Association of IL10, IL10RA, and IL10RB polymorphisms with benign prostate hyperplasia in Korean population. Association study of IL10 and IL23R-IL12RB2 in Iranian patients with Behcet's disease. [GWAS:...
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[GWAS:Behcet's disease]
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First genome-wide association study for this disorder, albeit of 152 patients, reports an association between this SNP (odds ratio 2.04, p = 4.2 x10e-5) and Behcet's disease.
Magnitude: 0
Frequency: 58.0%
References:11
Frequency: 58.0%
References:11
0.76x lower risk for spondylitis
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rs17482078 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.70 (p=1.2x10e-8). [GWAS:Behcet's disease]
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According to a 2010 report, each A allele at rs3024490 in the IL10 gene increased the risk of Behçet's disease about 1.4 times in a Turkish population.
0.5x decreased risk for endometriosis
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rs1800871(C) carriers are associated with a reduced endometriosis risk by approximately 2x compared with the common rs1800871(T;T) genotype in a study of 196 Chinese patients. rs2222202 (C/T) (p=0.03) and rs1800871 (C/T) (p=0.05) showed significant allelic associations with pediatric onset Crohn's disease. rs1800871(T) carriers were 3x more likely to have their pregnancies terminate early (<10 weeks) than (C) carriers, based on a study of ~500 pregnancies. In a study of 1,757 cases of Alzheimer's disease and 6,295 controls, an interaction was replicated between IL6 genotype rs2069837(A;A) and IL10 genotype rs1800871(C;C). The synergy factor (SF) was 1.63 (CI: 1.10-2.41, p = 0.01), controlling for age, gender and ApoE4 genotype. 23andMe reports that each G allele at rs1800871 is associat...
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
Magnitude: 0
Frequency: 81.5%
Repute:Good
References:14
Frequency: 81.5%
Repute:Good
References:14
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs17810546-G).] [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 10; CELIAC10] [GWAS:Celiac disease] [GWAS:Celiac disease]
15 snps
(hide) Beta Thalassemia
Repute:Good
References:1
References:1
Normal
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Beta Thalassemia https://www.23andme.com/you/journal/beta_thalassemia/techreport/ A new frameshift beta zero-thalassemia mutation (codons 27-28 +C) found in a Chinese family. The spectrum of beta-thalassemia mutations in Taiwan: identification of a novel frameshift mutation. The spectrum of beta-thalassemia genes in China and Southeast Asia. beta-Thalassemia in Chinese: use of in vivo RNA analysis and oligonucleotide hybridization in systematic characterization of molecular defects. Molecular basis and haematological characterization of beta-thalassaemia major in Taiwan, with a mutation of IVS-1 3' end TAG-->GAG in a Chinese patient.
References:1
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Identification of five rare mutations including a novel frameshift mutation causing beta zero-thalassemia in Thai patients with beta zero-thalassemia/hemoglobin E disease.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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rs33930165 is a relatively rare SNP found in the beta hemoglobin HBB gene, adjacent to the well-known SNP associated with malarial resistance (rs334). This SNP gives rise to the 'Hb C', or hemoglobin C, form of hemoglobin as the HBB forms are commonly named. It is found primarily in a subset of West Africa. rs33930165 is associated with increased malarial resistance, yet without giving rise to sickle cell anemia. A study of 4,000+ individuals in Burkina Faso found that rs33930165(A;G) heterozygotes had a 29% reduction in risk of clinical malaria (p = 0.0008), and rs33930165(C;C) homozygotes had a 93% reduction (p = 0.0011). [OMIM:?]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
normal
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rs33950507 is a SNP found in the beta hemoglobin HBB gene, not far from the well-known SNP associated with malarial resistance (rs334, Hb S). This SNP gives rise to the 'Hb E', or hemoglobin E, form of hemoglobin as the HBB forms are commonly named. It is found primarily in Southeast Asia. rs33950507(A) is associated with somewhat increased malarial resistance, and in homozygous (A;A) state, with mild hypochromic microcytic anemia. Microarray-based estimation of SNP allele-frequency in pooled DNA using the Langmuir kinetic model. [OMIM:?]
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
common in clinvar
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Beta Thalassemia https://www.23andme.com/you/journal/beta_thalassemia/techreport/
Magnitude: 0
Repute:Good
References:11
Repute:Good
References:11
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[OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
common in clinvar
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Beta Thalassemia https://www.23andme.com/you/journal/beta_thalassemia/techreport/
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
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[OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
common in clinvar
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Hb Monroe or alpha 2 beta 230(B12)Arg----Thr, a variant associated with beta-thalassemia due to A G----C substitution adjacent to the donor splice site of the first intron. Beta thalassemia due to a novel mutation in IVS 1 sequence donor site consensus sequence creating a restriction site. Expression of a beta thalassemia gene with abnormal splicing. Beta-thalassaemia in Cubans: novel allele increases the genetic diversity at the HBB locus in the Caribbean. Intrinsic differences between authentic and cryptic 5' splice sites. ThalassoChip, an array mutation and single nucleotide polymorphism detection tool for the diagnosis of beta-thalassaemia. A new mutation in IVS-1 of the human beta globin gene causing beta thalassemia due to abnormal splicing. The molecular basis of beta thalassaemia i...
common in complete genomics
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beta 0 thalassemia, a nonsense mutation in man. Human gene mutation database-a biomedical information and research resource. [OMIM:?]
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Beta Thalassemia https://www.23andme.com/you/journal/beta_thalassemia/techreport/ The beta-thalassaemia mutations in the population of Cyprus. Novel promoter and splice junction defects add to the genetic, clinical or geographic heterogeneity of beta-thalassaemia in the Portuguese population. Molecular basis of beta-thalassemia in Turkey: detection of rare mutations by direct sequencing. The peculiar spectrum of beta-thalassemia genes in Tunisia. beta-Thalassemia in American Blacks: novel mutations in the 'TATA' box and an acceptor splice site. Significance of borderline hemoglobin A2 values in an Italian population with a high prevalence of beta-thalassemia.
25 snps
(hide) Bicuspid aortic valve
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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rs41309764, also known as R1108X, is a SNP in the NOTCH1 gene. The common allele is rs41309764(C), while the rare rs41309764(T) allele encodes the variant. A normal human heart contains three valves. Carriers of one rs41309764(T) allele, such as Arnold Schwarzenegger, will develop an early developmental defect in the aortic valve leading to a bicuspid aortic valve, and without treatment, they are prone to progressive aortic valve disease in their later life due to calcification. [OMIM:?]
1 snp
(hide) Bipolar disorder
1.51x increased risk of developing bipolar disorder
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rs4027132 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (A), and the odds ratio associated with heterozygotes is 1.39 (CI 1.19-1.64), and for homozygotes, 1.51 (CI 1.27-1.79). [GWAS:None]
Increased risk of mental disorders
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rs16944 is a SNP in the interleukin 1, beta gene, a member of the cytokine family involved in the inflammatory response. The rs16944 G;G genotype is associated with risk for multiple mental illnesses. An increased risk for schizophrenia was found in a genetic association study of 2111 Caucasian individuals with an odds ratio of 1.24 (95% CI 1.09, 1.41) . Studies examining the brains of schizophrenic and bipolar individuals found reduced gray matter and hypoactivity associated with the G;G genotype. Additionally, this genotype is associated with impaired ability to achieve remission in a study of 256 Caucasian individuals with depression (odds ratio = 1.74; 95% confidence interval 1.2-4.3). The rs16944 A allele increases susceptibility to Osteoarthritis, with 1.80 times for heterozygotes (A...
Possibly reduced risk of Bipolar Disorder. This appears to lower the risk of Bipolar Disorder compared to the more common version of the gene, based on preliminary research.
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Linked to bipolar disorder in one of the most comprehensive studies in 2007. Risk allele with reference to dbSNP orientation is reported to be (T), with either one or two copies leading to an odds ratio of 2 (CI 1.6-2.7). Some replications, but in 2011 23andMe published as failed to replicate in Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Findings from bipolar disorder genome-wide association studies replicate in a Finnish bipolar family-cohort. Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies. [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample...
1.32x increased risk of developing bipolar disorder
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rs1375144, a SNP in the DPP10 gene, has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.32 (CI 1.07-1.63), and for homozygotes, 1.59 (CI 1.29-1.96). Findings from bipolar disorder genome-wide association studies replicate in a Finnish bipolar family-cohort. [GWAS:None]
Normal (higher) risk of Bipolar Disorder. This is the most common version of this SNP, so most people have this. But it is suspected of having a higher risk of Bipolar Disorder compared to the other rare versions of this SNP.
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Bipolar disorder failed to replicate in [PharmGKB:Non-Curated GWAS Results: A genome-wide association study implicates diacylglycerol kinase eta (DGKH) and several other genes in the etiology of bipolar disorder (Initial Sample Size: 461 cases, 563 controls; Replication Sample Size: 772 cases, 876 controls; Risk Allele: rs1012053-A).] [GWAS:Bipolar disorder]
1.1x increased risk for schizophrenia
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rs1344706 is a SNP in the ZNF804A gene, and it is probably the first SNP to have been reported as achieving genome-wide significance for psychosis. Reviews the literature, and concludes that rs1344706 is 'robustly, if modestly' associated with increased risk for schizophrenia. A genome-wide association study of schizophrenia (479 cases, 2,937 controls) followed by additional testing and a meta-analysis concluded that the strongest evidence for association was around ZNF804A (rs1344706; p = 1.61 x 10e-7) and that the finding was strengthened when the affected phenotype included bipolar disorder (p = 9.96 x 10e-9). Executive function, neural circuitry, and genetic mechanisms in schizophrenia. Apoptotic engulfment pathway and schizophrenia. Persistence criteria for susceptibility genes for sc...
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[GWAS:Bipolar disorder]
Frequency: 8.0%
References:3
References:3
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rs11098403 is an intergenic SNP on chromosome 4 located ~300kb upstream of the 5' end of the NDST3 gene. Although in one publication the rs11098403(G) allele is said to be associated with increased risk for schizophrenia (odds ratio of 1.4, at least in Ashkenazi Jews), in another report this same allele is associated with decreased risk (odds ratio 0.6, in Han Chinese).,
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Association between rs2799573 and psychiatric disorders was shown in a 2013 study by the Cross-Disorder Group of the Psychiatric Genomics Consortium . In this study, genome-wide SNP data consisting of 1,250,922 autosomal SNPs were analyzed to identify genetic variants associated with autism spectrum disorder, ADHD, bipolar disorder, major depressive disorder, and schizophrenia. 33,332 cases and 27,888 controls included both unrelated and family-based samples (trios). A multinomial logistic regression procedure was used to identify the best-fitting model of relations between genotype and phenotype. This SNP, on chromosome 10 in an intron of CACNB2, was one of four genome-wide significant signals associated with the five psychiatric disorders (p = 4.29 x 10-8). The risk allele T exhibited al...
Frequency: 15.3%
References:1
References:1
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[GWAS:Bipolar disorder]
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[GWAS:Bipolar disorder]
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Bipolar I disorder and schizophrenia: a 440-single-nucleotide polymorphism screen of 64 candidate genes among Ashkenazi Jewish case-parent trios. RGS4 mRNA expression in postmortem human cortex is associated with COMT Val158Met genotype and COMT enzyme activity. RGS4 is not a susceptibility gene for schizophrenia in Japanese: association study in a large case-control population. Association of RGS2 and RGS5 variants with schizophrenia symptom severity. Interaction between interleukin 3 and dystrobrevin-binding protein 1 in schizophrenia. Association of RGS4 variants with schizotypy and cognitive endophenotypes at the population level. A genome-wide investigation of SNPs and CNVs in schizophrenia. [PharmGKB:Curated This variant is associated with differential antipsychotic treatment respon...
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Along with rs6442925 and rs534654, this SNP, rs1534891, is part of a 3-SNP (multi-locus) interaction that is associated with bipolar disorder.
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[PharmGKB:Non-Curated GWAS results: Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder (Initial Sample Size: 1,098 cases, 1,267 controls; Replication Sample Size: 4,387 cases, 6,209 controls). This variant is associated with Bipolar disorder.] [GWAS:Bipolar disorder]
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[GWAS:Bipolar disorder]
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Associated with bipolar disorder in individuals of European ancestry. [GWAS:Bipolar disorder and schizophrenia]
Frequency: 19.5%
References:4
References:4
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[PharmGKB:Non-Curated GWAS Results: Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder (Initial Sample Size: 1,098 cases, 1,267 controls; Replication Sample Size: 4,387 cases, 6,209 controls; Risk Allele: rs12290811-A). This variant is associated with Bipolar disorder.] [GWAS:Bipolar disorder] [GWAS:Bipolar disorder]
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: 'Haplotype association analysis suggests that the haplotype CCGCA (at SNPs rs3125, rs6314, rs1923886, rs2224721 and rs2770296) is protective against bipolar disorder (P = 0.021, odds ratio 0.63) and the rarer haplotype CCACG confers risk to the disorder (P = 0.0065, odds ratio 3.08).' Genetic variation in the serotonin 2A receptor and suicidal ideation in a sample of 270 Irish high-density schizophrenia families.
Frequency: 24.8%
References:3
References:3
1.5x risk
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rs10982256 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.26 (CI 1.08-1.47), and for homozygotes, 1.47 (CI 1.24-1.74). [GWAS:None]
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[GWAS:Bipolar disorder]
1.5x increased risk for bipolar disorder
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rs131690, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for bipolar disorder. The odds ratio for carriers of the minor allele (G) are reported as 1.50 (CI:1.14 - 2.03, p=0.0063) based on a study of 171 Japanese patients.
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associated with bipolar disorder
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[GWAS:Bipolar disorder]
1.8x risk
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rs2953145 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.84 (CI 1.31-2.58), and for homozygotes, 2.14 (CI 1.53-2.98). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,868 cases, 2,938 controls; Replication Sample Size: NR; Risk Allele: rs2953145-C). This variant is associated with bipolar disorder.] [GWAS:Bipolar disorder]
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journal When using lithium as a treatment for Bipolar disorder rs9784453 appears to be associated with time to recurrence of a mood episode while on. By my reading of Figure 3, the median time to recurrence is about 230 days for homozygote carriers with the 'poor response' allele and about 520 days for homozygote carriers with the 'good response' allele, with heterozygote carriers falling in between.
Frequency: 33.6%
References:3
References:3
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blog Association of Circadian Genes with Mood Disorders *rs2287161 *rs10462028 *rs11123857 *rs17083008 *rs885861
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[GWAS:Bipolar disorder]
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: 'Haplotype association analysis suggests that the haplotype CCGCA (at SNPs rs3125, rs6314, rs1923886, rs2224721 and rs2770296) is protective against bipolar disorder (P = 0.021, odds ratio 0.63) and the rarer haplotype CCACG confers risk to the disorder (P = 0.0065, odds ratio 3.08).'
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[GWAS:Bipolar disorder]
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[GWAS:Bipolar disorder]
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[PharmGKB:Non-Curated GWAS results: Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder (Initial Sample Size: 1,098 cases, 1,267 controls; Replication Sample Size: 4,387 cases, 6,209 controls). This variant is associated with Bipolar disorder.] [GWAS:Bipolar disorder]
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23andMe blog () rs1006737 or (rs2159100) Each T at this SNP increased the odds of bipolar disorder by 1.18 times compared to having two CC copies
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[GWAS:Bipolar disorder]
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: 'Haplotype association analysis suggests that the haplotype CCGCA (at SNPs rs3125, rs6314, rs1923886, rs2224721 and rs2770296) is protective against bipolar disorder (P = 0.021, odds ratio 0.63) and the rarer haplotype CCACG confers risk to the disorder (P = 0.0065, odds ratio 3.08).' Pharmacogenetics of antidepressant response.
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13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. *rs751229(T) and rs3738401(A) was over-transmitted to males with psychotic disorder. *under-transmitted rs821616(T) and rs1411771(T) *The risk haplotype for psychotic disorder also associated to perseverations (P = 0.035; for rs751229 alone P = 0.0012), and a protective haplotype G-T-G with rs1655285 in addition to auditory attention (P = 0.0059).
1.2x risk
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rs1344484 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.24 (CI 1.03-1.48), and for homozygotes, 1.52 (CI 1.27-1.82). Findings from bipolar disorder genome-wide association studies replicate in a Finnish bipolar family-cohort. [GWAS:None]
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rs3847953 and rs933399 associated with bipolar disorder [OMIM:MAJOR AFFECTIVE DISORDER 1; MAFD1]
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[GWAS:Bipolar disorder]
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Common variants in the ATM, BRCA1, BRCA2, CHEK2 and TP53 cancer susceptibility genes are unlikely to increase breast cancer risk. LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs.
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[GWAS:Bipolar disorder]
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[GWAS:Bipolar disorder]
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Associated with bipolar disorder in individuals of African ancestry.
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[GWAS:Bipolar disorder]
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rs3847953 and rs933399 associated with bipolar disorder [OMIM:MAJOR AFFECTIVE DISORDER 1; MAFD1]
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rs1556314 associated with bipolar disorder type I *C-T-A haplotype of SNPs rs1618355(C), rs933151(T), and rs749909(A) was significantly associated with early age at onset in BD-I families
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[GWAS:Bipolar disorder]
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[GWAS:Bipolar disorder]
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13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. *rs980989 psychomotor processing speed
Frequency: 67.0%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder (Initial Sample Size: 1,098 cases, 1,267 controls; Replication Sample Size: 4,387 cases, 6,209 controls). This variant is associated with Bipolar disorder.] [GWAS:Bipolar disorder]
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rs1556314 associated with bipolar disorder type I *C-T-A haplotype of SNPs rs1618355(C), rs933151(T), and rs749909(A) was significantly associated with early age at onset in BD-I families [OMIM:TRANSIENT RECEPTOR POTENTIAL CATION CHANNEL, SUBFAMILY M, MEMBER 2;]
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In a survey that scanned 80 genes, no SNPs with a large effect were found to be associated with bipolar disorder. However, the SNP with the largest association was rs1170191, in first intron of the diacylglycerol kinase eta DGKH gene. The odds ratio for the risk allele of this SNP is 1.59 (p = 1.5x10e-8, experiment-wide p<0.01).
normal risk
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rs140504, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for bipolar disorder. The odds ratio for carriers of the minor allele (G) are reported as 1.45 (CI:1.11 - 1.84, p=0.0054) based on a study of 171 Japanese patients. [OMIM:MAJOR AFFECTIVE DISORDER 1; MAFD1]
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[GWAS:Bipolar disorder]
Frequency: 77.9%
References:0
References:0
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Associated with bipolar disorder in individuals of European ancestry.
Frequency: 78.8%
References:1
References:1
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rs1556314 associated with bipolar disorder type I *C-T-A haplotype of SNPs rs1618355(C), rs933151(T), and rs749909(A) was significantly associated with early age at onset in BD-I families
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anxiety-related personality traits, ADHD, schizophrenia part of a three marker haplotype rs737865-rs4680-rs165599 epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes popular in pubmed is associated with bipolar disorder and influences prefrontal aspects of verbal memory in bipolar patients and healthy controls. [PharmGKB:Curated In a study of 78 African American and 65 white patients diagnosed with schizophrenia or schizoaffective disorder, this SNP in the COMT gene was found to have significant associations with response to risperidone over 2-12 weeks in both African-American and white patients.] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
later onset of BP
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Although not associated with increased risk for developing bipolar disorder, amongst those with it, the (G) allele of this SNP has been reported to have a somewhat protective effect in that individuals who have a (G) allele develop bipolar disorder at a later age than those with the more common (A;A) genotypes. Also known as the -50T/C SNP from this GSK3-beta (GSK3B) gene. may effect lithium treatment response - C allele carriers showed considerably greater response with lithium treatment, with remissions of 56.25% after 4 weeks compared to 31% for T/T carriers [PharmGKB:Curated This variant is in the promoter region of GSK3B. T allele is associated with greater transcription activity compared with the A allele. This variant is associated with antidepressant treatment response in Chinese ...
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13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. *rs751229(T) and rs3738401(A) was over-transmitted to males with psychotic disorder. *under-transmitted rs821616(T) and rs1411771(T) *The risk haplotype for psychotic disorder also associated to perseverations (P = 0.035; for rs751229 alone P = 0.0012), and a protective haplotype G-T-G with rs1655285 in addition to auditory attention (P = 0.0059). [OMIM:SCHIZOPHRENIA, SUSCEPTIBILITY TO]
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[GWAS:Bipolar disorder]
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[GWAS:Bipolar disorder]
normal
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Women with two rs821616(T) SNPs seem to experience more rapid cognitive decline as they age compared to men. 13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. *rs821616 verbal fluency
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13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. *rs751229(T) and rs3738401(A) was over-transmitted to males with psychotic disorder. *under-transmitted rs821616(T) and rs1411771(T) *The risk haplotype for psychotic disorder also associated to perseverations (P = 0.035; for rs751229 alone P = 0.0012), and a protective haplotype G-T-G with rs1655285 in addition to auditory attention (P = 0.0059).
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[GWAS:Bipolar disorder]
This genotype is normal for caucasians, but is reported to have 1.5x increased risk for bipolar disorder in one small study of japanese patients.
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rs131702, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for bipolar disorder. The odds ratio for carriers of the minor allele (G) are reported as 1.49 (CI:1.15 - 1.93, p=0.0026) based on a study of 171 Japanese patients.
normal
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rs4276227 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.2 (CI 0.99-1.46), and for homozygotes, 1.49 (CI 1.23-1.81).
Magnitude: 0
Frequency: 8.2%
References:2
Frequency: 8.2%
References:2
normal
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rs11622475 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.13 (CI 0.89-1.44), and for homozygotes, 1.47 (CI 1.17-1.86). [GWAS:None]
normal
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rs7757037, a SNP in the FKBP5 gene, is associated with increased risk for bipolar disorder in a study of 500+ Caucasian patients. The most common allele, rs7757037(G), was associated with highest risk. Giving that allele a relative odds ratio of 1.0, the odds for the (A;G) and (A;A) genotypes were 0.68x (CI:0.53-0.87, p=0.007) and 0.63x (CI: 0.45-0.89, p=0.007).
common in clinvar
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rs3738401 is a SNP in the DISC1 gene, known as R264Q. Associated with schizophrenia 13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. *rs751229(T) and rs3738401(A) was over-transmitted to males with psychotic disorder. *under-transmitted rs821616(T) and rs1411771(T) *The risk haplotype for psychotic disorder also associated to perseverations (P = 0.035; for rs751229 alone P = 0.0012), and a protective haplotype G-T-G with rs1655285 in addition to auditory attention (P = 0.0059). [OMIM:DISRUPTED IN SCHIZOPHRENIA 1; DISC1]
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23andMe blog rs1006737 or (rs2159100) Each T at this SNP increased the odds of bipolar disorder by 1.18 times compared to having two CC copies [PharmGKB:Curated A genome-wide association analysis study in 4,387 cases and 6,209 controls identified a strong association of this variant in the CACNA1C gene with bipolar disorder.] [OMIM:MAJOR AFFECTIVE DISORDER 9; MAFD9] [GWAS:Bipolar disorder]
1.4x risk
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rs6458307 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 0.84 (CI 0.75-0.96), and for homozygotes, 1.39 (CI 1.13-1.69). [PharmGKB:Non-Curated GWAS results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,868 cases, 2,938 controls; Replication Sample Size: NR). This variant is associated with Bipolar disorder.] [GWAS:Bipolar disorder]
normal
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rs3761218 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 0.97 (CI 0.81-1.15), and for homozygotes, 1.31 (CI 1.09-1.57). Findings from bipolar disorder genome-wide association studies replicate in a Finnish bipolar family-cohort. [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,868 cases, 2,938 controls; Replication Sample Size: NR; Risk Allele: rs3761218-C). This variant is associated with bipolar disorder.] [GWAS:None] [GWAS:Bipolar disorder]
0.47x decreased risk for bipolar disorder
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rs4713902, a SNP in the FKBP5 gene, is associated with increased risk for bipolar disorder in a study of 500+ Caucasian patients. The most common allele, rs4713902(T), was associated with highest risk. Giving that allele a relative odds ratio of 1.0, the odds for the (C;T) and (C;C) genotypes were 0.69x (CI:0.55-0.88, p=0.001) and 0.47 (CI: 0.30-0.74, p=0.001).
normal
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rs7570682 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.23 (CI 1.09-1.40), and for homozygotes, 1.64 (CI 1.28-2.12). [GWAS:None]
common/normal Val/val (normal) variant of the Val66Met snp in the BDNF gene that codes for brain-derived neurotrophic factor. Met/met is associated with susceptibility to neuropsychiatric disorders.
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
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located in promoter region of BDKRB2 - associated with panic disorder, bipolar disorder, and substance abuse Identification of functional SNPs in the 5-prime flanking sequences of human genes.
common on affy axiom data
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rs2230912, also known as Q460R, is a SNP in the purinergic receptor P2X, ligand-gated ion channel, 7 P2RX7 gene. This SNP has been reported to be associated with increased risk for bipolar disorder in one study , but the association was not replicated in a large UK case-control sample (bipolar I disorder N = 687, unipolar recurrent major depression N = 1,036, controls N = 1,204). The G allele is the putative risk allele. Analysis of single nucleotide polymorphisms in genes in the chromosome 12Q24.31 region points to P2RX7 as a susceptibility gene to bipolar affective disorder. P2RX7, a gene coding for a purinergic ligand-gated ion channel, is associated with major depressive disorder. Association between depression and the Gln460Arg polymorphism of P2RX7 gene: a dimensional approach. P2RX7...
common in complete genomics
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rs1156044(A) was significantly associated with bipolar disorder (p = 0.013) but differed in allele (rs1156044 G allele) from that previously reported as associated with BD.
normal
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rs683395 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.47 (CI 1.26-1.71), and for homozygotes, 1.3 (CI 0.69-2.46). Findings from bipolar disorder genome-wide association studies replicate in a Finnish bipolar family-cohort. [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,868 cases, 2,938 controls; Replication Sample Size: NR; Risk Allele: rs683395-G). This variant is associated with bipolar disorder.] [GWAS:Bipolar disorder]
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23andMe blog () rs10994336 or (rs4948418) Each T at this SNP increased the odds of developing bipolar disorder by 1.45 times compared to the CC genotype. [GWAS:None]
Magnitude: 0
Frequency: 83.9%
References:1
Frequency: 83.9%
References:1
normal
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rs10134944 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.45 (CI 1.24-1.68), and for homozygotes, 1.32 (CI 0.74-2.33). [GWAS:None]
Magnitude: 0
Frequency: 86.2%
Repute:Good
References:24
Frequency: 86.2%
Repute:Good
References:24
common on affy axiom data
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23andMe blog rs10994336 or (rs4948418) Each T at this SNP increased the odds of developing bipolar disorder by 1.45 times compared to the CC genotype. This is one of the SNPs reported by NutraHacker. [PharmGKB:Curated GWAS Results: Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder (Initial Sample Size: 1,098 cases, 1,267 controls; Replication Sample Size: 4,387 cases, 6,209 controls; Risk Allele: rs10994336-T). This variant is associated with Bipolar disorder.] [OMIM:MAJOR AFFECTIVE DISORDER 8; MAFD8] [GWAS:Bipolar disorder]
higher risk for RA
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rs6314, also known as C1354T or His452Tyr/H452Y, is a SNP in the serotonin 2A receptor HTR2A gene. Based on a study of 166 Caucasian patients being treated for depression with paroxetine, rs6314 heterozygotes were associated with better response. There was a significantly higher frequency of heterozygotes in the remitter and response groups in comparison to the non-remitter (odds ratio 7.50, p=0.002) and non-response groups (odds ratio 5.25, p=0.01). * rs6314 is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6314(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs13286...
Magnitude: 0
Frequency: 89.4%
Repute:Good
References:2
Frequency: 89.4%
Repute:Good
References:2
normal
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rs10937823 is a SNP associated with the gene SORCS2, variants of which may play a role in bipolar disorder. The allele most frequently occurring is C, and the variant is T. In the HapMap-CEU population, CC, CT, and TT genotype frequencies were 0.894, 0.097, and 0.009, respectively. However, in the HapMap-CHB population, CT was the most frequently expressed genotype; CC, CT, and TT genotype frequencies were 0.366, 0.439, and 0.195, respectively. In some sample populations, the TT genotype did not exist (TSI, MKK, LWK, ASW). [dbSNP] The SORCS2 (sortillin-related VPS10 domain containing receptor 2) gene on chromosome 4p16.1 is found to be highly expressed in the mature human brain and kidney. High levels of expression are also seen in the brain during mouse development. [GeneCards] This gene ...
normal
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rs2609653 has been reported in a large study to be associated with bipolar disorder. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.43 (CI 1.19-1.71), and for homozygotes, 3.62 (CI 1.26-10.44). [GWAS:None]
common for Caucasians on the 23andme platform
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rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission paper Association with and bipolar disorder in a Northern Swedish, Isolated Population. 182 patients and 364 unrelated control individuals. P = .001 rs11178997 significantly reduced TPH2 transcriptional activity by 22% and 7% in cell lines might have implications for the development and function of the serotonergic system in the brain. paper Carriers of the A-Allele of rs11178997 showed a decreased cortisol and ACTH stimulation. might be crucial factors for major depression pdf paper associated with bipolar disorder Minor allele yielded odds ratio of 1.5 (CI:1.2-1.9) for increased risk for bipolar disorder in a study of 883 Russian patients. Transmission disequilibrium of polymorphic variants in the tryp...
92 snps
(hide) Bladder cancer
1.6x increased risk for prostate cancer; also other cancers 1.4 times as likely to develop colorectal cancer
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. This SNP has also been reported to influence the cancer-risk-decreasing effect of aspirin. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neig...
increased risk of gastric and bladder cancer
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rs2976392 and diffuse-type gastric cancer (allele-specific odds ratio (OR) = 1.62, 95% CI = 1.38-1.89, P = 1.11 x 10(-9)). Substitution of the C allele with the risk allele T at a SNP in the first exon (rs2294008, which has r(2) = 0.995, D' = 0.999 with rs2976392) reduces transcriptional activity of an upstream fragment of the gene [OMIM:PROSTATE STEM CELL ANTIGEN; PSCA] [GWAS:Bladder cancer]
1.5x increased bladder cancer risk
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rs9642880 is a SNP located in chromosome region 8q24, a region that has been linked to prostate, breast, and colon cancer. A study ultimately totaling over 4,000 bladder cancer patients of European ancestry (and 40,000 controls) concluded that individuals carrying two copies of rs9642880(T) were at 1.49x increased risk (allele-specific odds ratio = 1.22, p = 9 x 10e-12) for the disease. This SNP was not associated, however, with risk for prostate, breast, or colon cancer. Another study in Chinese populations found similar results in regard to bladder cancer. rs9642880(T;T) estimated risk of developing 1.49 times that of noncarriers. 1,803 urinary bladder cancer cases and 34,336 controls. No association with prostate, colorectal and breast cancers. In contrast to GSTM1 SNPs, the rs9642880(T...
Normal risk of developing bladder cancer. This is the normal risk of bladder cancer, particularly in Europeans and in people who already have tumors with low risk of progression.
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rs710521 is a SNP located in chromosome region 3q38, near the TP63 gene. A study ultimately totaling over 4,000 bladder cancer patients of European ancestry (and 40,000 controls) concluded that individuals carrying two copies of rs710521(A) were at 1.4x increased risk (allele-specific odds ratio = 1.19, p = 1 x 10e-7) for the disease. An additional 1,425 bladder cancer patients, supplemented by a meta-analysis of 5,695 additional cases (and 40,000+ controls), did replicate a (somewhat) increased risk associated with the rs710521(A) allele. The overall odds ratio was 1.18 (OR: 1.12 - 1.25, p < 0.0001). Another study in Chinese populations did not find an increased risk of bladder cancer for this SNP. [PharmGKB:Non-Curated GWAS Results: Sequence variant on 8q24 confers susceptibility to ...
~1.2x increased risk for several types of cancer
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rs401681 is a SNP in the CLPTM1-like CLPTM1 gene. The following studies span several types of cancer, and over 30,000 cases and 45,000 controls. deCODE press release reports rs401681 linked to basal cell carcinoma and many cancers for individuals with shorter telomeres, whereas those with long telomeres are at greater risk of melanoma. Neighboring rs2736098 also increases risk of cancer by affecting telomerase reverse transcriptase. The risk of these different cancers conferred by these two SNPs appears to be independent. 23andMe blog rs2736098 and rs401681 linked to many cancers, including susceptibility to pancreatic cancer However, a very large study (encompassing thousands of cases and controls) found no association between rs401681 and either (1) mean telomere length, or, (2) breast c...
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[GWAS:Bladder cancer]
Frequency: 39.8%
References:14
References:14
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[GWAS:Celiac disease]
Frequency: 41.7%
References:1
References:1
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[GWAS:Bladder cancer]
increased risk for bladder cancer if part of risk haplotype
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rs760805, a SNP in the RUNX3 gene, has been reported to be the most significantly associated with risk for bladder cancer of several SNPs in this gene, based on a study of 368 Chinese patients. The adjusted odds ratio for the rs760805(A;A) genotype is 1.97 (CI: 1.44-2.69). Further investigation of this region in this same study indicated that 4 other SNPs in the RUNX3 gene, as well as smoking, are associated with increased risk for bladder cancer. In particular, 2 haplotypes, both containing the rs760805(A) allele, were associated with 2-3x increased risk. An individual carrying the risk forms of all 5 RUNX3 SNPs and also smoking had on average an odds ratio for bladder cancer that was 6.37 fold higher than average (CI: 4.57-8.87, p = 7.03 x 10(-28)).
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[GWAS:Bladder cancer]
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[GWAS:Bladder cancer]
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[GWAS:None]
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[GWAS:None]
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[GWAS:Bladder cancer]
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[GWAS:None]
normal
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rs2228000, also known as Ala499Val and A499V, is a SNP in the DNA nuclear excision repair gene xeroderma pigmentosum complementation group C XPC gene. The Val (V) allele is encoded by the rs2228000(T) allele. A meta-analysis of 11 studies with 5581 cancer cases and 6351 controls concluded that rs2228000(T;T) homozygotes had an increased overall cancer risk (odds ratio of 1.24, CI: 1.08-1.42) compared with (C;C) homozygotes. This was primarily a risk for bladder cancer.
0.68x decreased risk for bladder cancer
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rs5275, also known as exon1-+837T>C, is a SNP in the PTGS2 gene. A study of 635 Caucasian bladder cancer patients found a reduced risk associated with the minor (C) allele of rs5275, (odds ratio 0.68, CI: 0.54-0.87, p=0.002, remaining significant after multiple comparison adjustment). (T;T) genotype of PTGS2 8473T>C (rs5275) was significantly correlated with a better survival when compared to the combined T/C and C/C genotype (Hazard ratio [HR] = 0.47; P value = 0.046 and HR = 0.16; P = 0.013, respectively) in colorectal cancer Allellic variants in regulatory regions of cyclooxygenase-2: association with advanced colorectal adenoma. Association of frequent consumption of fatty fish with prostate cancer risk is modified by COX-2 polymorphism. Cyclooxygenase-2 polymorphisms in Parkinso...
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[GWAS:Bladder cancer]
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The T allele at rs798766 is associated with 1.24 higher odds of bladder cancer. [OMIM:?] [GWAS:Urinary bladder cancer]
common in complete genomics Predicted to be a NAT2 slow metabolizer.
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With 99% sensitivity and 95% specificity, at least in Caucasian populations, rs1495741 is reported to classify the NAT2 phenotype of an individual; it therefore is a candidate to replace the 7-SNP panel used in genosets such as gs138, gs139, and gs140. The rs1495741(A;A), (A;G) and (G;G) genotypes predicted slow, intermediate, and rapid NAT2 acetylation phenotypes, respectively. [GWAS:None]
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rs868 is a SNP in the transforming growth factor, beta receptor I TGFBR1 gene. A total of 1,157 Spanish cases with urothelial cell carcinoma of the bladder and 1,157 matched controls were analyzed for TGFBR1 SNP associations, and among patients with muscle-invasive bladder cancer tumors, a significant association between rs868 and disease-specific mortality was found, with an allele dosage effect (p-trend = 0.003).
normal
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rs1136410, also known as V762A, is a SNP in the PARP1 Poly(ADP-ribose) polymerase-1 gene. The rs1136410(C) allele encodes the less common A (alanine) amino acid at this codon. A study of 1,000 glioblastoma multiforme cases and 2,000 controls in the US concluded that the PARP1 gene rs1136410(C) allele was associated with a 20% reduction in risk for glioblastoma multiforme (odds ratio 0.80, CI: 0.67-0.95). A meta-analysis of 21 studies with 12,027 cancer patients found no significant association overall between rs1136410 and cancer risk, however, in the stratified analyses, rs1136410(C) was associated with an increased risk of cancer among Asian populations (CT + CC vs. TT: odds ratio 1.11, CI: 1.01-1.23, p(heterogeneity) = 0.210), but a decreased risk of cancer (CT + CC vs. TT: odds ratio 0...
Magnitude: 0
Frequency: 78.8%
Repute:Good
References:5
Frequency: 78.8%
Repute:Good
References:5
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Rs11892031[A] on chromosome 2q37 in an intronic region of the UGT1A locus is associated with urinary bladder cancer risk. [GWAS:None]
normal
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rs6869366, also known as G-1394T, is a SNP in the DNA repair XRCC4 gene. A study of 158 Taiwanese patients found an association between carriers of a rs6869366(G) allele and increased risk for bladder cancer. The odds ratio was 2x for heterozygotes; no (T;T) homozygotes were seen in this study. Risk was further studied based on smoking history. Smokers who were also rs6869366(T) carriers were at even higher risk (crude OR=3.29, CI: 1.21-8.90, adjusted OR=3.35, CI=1.41-8.49), implying a gene-smoking interaction.
25 snps
(hide) Blood
blood type O
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=Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women. |OA=23andMe blog each copy rs505922(C) is associated with 1.2x risk of pancreatic cancer influences ABO blood group [PharmGKB:Non-Curated GWAS results: Common susceptibility allele are unlikely to contribute as strongly as the FV and ABO loci to VTE risk: results from a GWAS approach. (Initial Sample Size: 419 cases, 1,228 controls; Replication Sample Size: 1,757 cases, 1,480 controls); (Region: 9q34.2; Reported Gene(s): ABO; Risk Allele: rs505922-C); (p-value= 0.000000000000004).This variant is associated with Venous thromboembolism.] [OMIM:?] [GWAS:Venous thromboembolism]
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This SNP is a variant in the ABO gene, and is therefore potentially useful in determining ABO blood group, such as through the use of genosets.
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[OMIM:DOMBROCK BLOOD GROUP]
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This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes. Histo-blood group gene polymorphisms as potential genetic modifiers of infection and cystic fibrosis lung disease severity. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. [GWAS:Serum alkaline phosphatase levels]
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This SNP is in the ABO gene, and is therefore potentially useful in determing ABO blood group, such as through the use of genosets.
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This SNP is a variant in the ABO gene, and is therefore potentially useful in determining ABO blood group, such as through the use of genosets.
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This SNP is a variant in the ABO gene, and is therefore potentially useful in determining ABO blood group, such as through the use of genosets.
Duffy-positive This genotype is associated with European populations and southwestern Native American populations.
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rs2814778 is within the DARC gene, which encodes the Duffy blood group antigen . This SNP shows an almost perfectly fixed difference in frequency between Europeans and those with African ancestry. (One exception appears to be a certain population of Czech gypsies, and certain non-Ashkenazi Jewish populations.) Additionally the Namibian San samples of the CEPH-HGDP are, uncharacteristically for Africans, all AA homozygotes for this SNP. The rs2814778 (G) allele is associated with African populations, while rs2814778 (A) is associated with European populations and southwestern Native American populations. rs2814778(G;G) protect against Plasmodium vivax malaria and predicts of white blood cell and neutrophil count 23andMe blog discussion Malaria Resistance (Duffy Antigen) [PharmGKB:Curated A...
References:2
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[OMIM:LUTHERAN BLOOD GROUP POLYMORPHISM Lu(a)/Lu(b)]
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The T allele of this SNP is associated with higher risk of pancreatic cancer. Phosphodiesterase 8B gene variants are associated with serum TSH levels and thyroid function. Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. Genetic variants associated with Von Willebrand factor levels in healthy men and women identified using the HumanCVD BeadChip. [PharmGKB:Non-Curated GWAS results: Population-based genome-wide association studies reveal six loci influencing plasma levels of live...
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[GWAS:Coagulation factor levels]
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ABO blood group rs8176719 represents a site in the ABO gene, and is a key SNP in determining blood group type O status. An allele that encodes either a blood group type A or type B will have a (G) at this SNP site, i.e. such an allele will be rs8176719(G). If a one-base deletion has occured at this site, removing this nucleotide all together, the corresponding allele is considered to be rs8176719(-) and encodes the most common blood group type O allele. However, an individual will typically only be blood group type O if they are carry two copies of (are homozygous) for this deletion, in other words, if their genotype is rs8176719(-;-). If they carry one copy, they could be blood type A, or blood type B (but are unlikely to be type O). A person who is rs8176719(G;G) is likely to be of blood...
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This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. This particular SNP can be useful in determining whether an ABO type A allele is more specifically an A1 type allele or an A2 type allele. The more common allele (80% of A types on average) is A1, consistent with having a rs8176750(C) allele, with the rarer A2 allele encoded by the deletion form rs8176750(-). This is the key defining characteristic between an A1 and an A2 allele.
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This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. ABO Blood Type [OMIM:?]
Not blood group B
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This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. ABO Blood Type
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This SNP is in the ABO gene, and is therefore potentially useful in determing blood group type, such as through the use of genosets. ABO Blood Type [OMIM:?] [GWAS:End-stage coagulation]
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This SNP is a variant in the ABO gene, and is therefore potentially useful in determining ABO blood group, such as through the use of genosets. 23andMe reports this as a G/T while decodeme reports it as a an A/C. [PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: Angiotensin converting enzyme activity was increased per copy of the rs8176746 A allele. Carriage of the A allele is associated with the B blood group antigen. Study size: 623 Study population/ethnicity: Academia Sinica Multi-Centered Young-Onset Hypertension (AS-YOH) Genetic Study; Han Chinese individuals with Hypertension. Significance metric(s): p = 9.3 × 10−5 Type of association: PD] [OMIM:?] [GWAS:Hematological and biochemical traits]
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This SNP is in the ABO gene, and is therefore potentially useful in determing ABO blood group, such as through the use of genosets. [GWAS:Tumor biomarkers]
common
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DNA-based methods in the immunohematology reference laboratory. Molecular basis of the Kell (K1) phenotype. Non-ABO Blood Groups [OMIM:KELL K/k BLOOD GROUP POLYMORPHISM]
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23andMe blog relevant for blood transfusion compatibility. venous thromboembolism, [OMIM:SOLUTE CARRIER FAMILY 44, MEMBER 2; SLC44A2]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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Influences ABO blood group ABO Blood Type
26 snps
(hide) Blood pressure
increased risk for celiac disease increased resistance to bacterial infections
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rs3184504 is a nonsynonymous SNP in the SH2B3 gene, and it is also known as R262W. In a recent (2008) study of non-HLA SNP associations of 1600+ celiac disease patients, this SNP was considered one of the most significant. The odds ratio for the minor allele was 1.19 (CI:1.10-1.30, p=1.33x10e-7). rs653178, another SNP in strong linkage disequilibrium (r<sup>2</sup>>0.99) with rs3184504, was also associated with celiac disease. associated with type-1 diabetes 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 23andMe blog blood pressure Pharmacogenetic implications for eight common blood pressure-associated...
Magnitude: 1.1
Frequency: 100.0%
References:1
Frequency: 100.0%
References:1
Normal (higher) blood pressure. Almost all white people and a majority of non-white people have this normal version. But it isn't as good as the other rare mutant version which would have lowered blood pressure. Tested in Asians. They had an average blood pressure of 127.4/80.1 with this Allele.
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The minor (G) allele of SNP rs10495584 was associated with lower mean systolic and diastolic blood pressures in men (121.1 +/- 14.2 and 76.3 +/- 10.2 mm Hg vs. 127.4 +/- 15.2 and 80.1 +/- 10.5 mm Hg, P = 0.002 and 0.007, respectively), but not in women (P > 0.05), and remained significant after correction for numerous other factors. However, its effect may be caused by a nearby, tightly linked SNP, rs11524.
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23andMe blog blood pressure [GWAS:Diastolic Blood Pressure]
Frequency: 9.7%
References:1
References:1
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diastolic blood pressure being the quantitative trait associated with in [GWAS:Quantitative traits]
Frequency: 16.8%
References:2
References:2
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23andMe blog blood pressure Confirmation of top polymorphisms in hypertension genome wide association study among Han Chinese. Pharmacogenetic implications for eight common blood pressure-associated single-nucleotide polymorphisms. [GWAS:Diastolic Blood Pressure]
Frequency: 21.2%
References:1
References:1
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[GWAS:Blood pressure]
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diastolic blood pressure [PharmGKB:Non-Curated GWAS results: Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness (Initial Sample Size: 644-1,327 individuals, depending on measure (Framingham); Replication Sample Size: NR). This variant is associated with Blood pressure.] [GWAS:Blood pressure]
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[GWAS:Blood pressure]
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diastolic blood pressure [GWAS:Blood pressure]
Frequency: 26.8%
References:7
References:7
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23andMe blog blood pressure High Blood Pressure (Hypertension) [GWAS:Diastolic Blood Pressure]
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[GWAS:Blood pressure]
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23andMe blog blood pressure [GWAS:Diastolic Blood Pressure]
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23andMe blog blood pressure High Blood Pressure (Hypertension) [GWAS:Diastolic Blood Pressure]
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23andMe blog blood pressure [GWAS:Diastolic Blood Pressure]
lower blood pressure
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A study of ~15,000 Europeans found that increased circulating natriuretic peptide and thus lower blood pressure and hypertension were associated with SNPs rs17376328(A), rs5068, rs198358(C), rs632793(G) 23andMe blog Natriuretic peptide system gene variants are associated with ventricular dysfunction after coronary artery bypass grafting. Dissecting complex traits: recent advances in hypertension genomics. Novel associations of CPS1, MUT, NOX4, and DPEP1 with plasma homocysteine in a healthy population: a genome-wide evaluation of 13 974 participants in the Women's Genome Health Study. Association of common variants in NPPA and NPPB with blood pressure does not translate into kidney damage in a general population study. Association of genetic variation in the natriuretic peptide system with...
Frequency: 41.6%
References:0
References:0
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23andMe blog blood pressure
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diastolic blood pressure being the quantitative trait associated with in [GWAS:Quantitative traits]
normal
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rs6749447 is a SNP in the serine threonine kinase 39 STK39 gene. A study of ~1,000 Amish originally identified rs6749447 and another SNP also in the STK39 gene, rs3754777, as being significantly associated with hypertension. This association was then found to also hold in patient data analyzed from the Framingham Heart Study and the Diabetes Genetics Initiative. On average, each minor allele, in this case rs6749447(G), is associated with 2.0 mmHg higher systolic blood pressure and a 1.0 mm Hg higher diastolic pressure. [PharmGKB:Non-Curated GWAS results: Whole-genome association study identifies STK39 as a hypertension susceptibility gene. (Initial Sample Size: 542 individuals; Replication Sample Size: 6,583 individuals); (Region: 2q24.3; Reported Gene(s): STK39; Risk Allele: rs6749447-G)...
Frequency: 48.1%
References:1
References:1
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[GWAS:Systolic blood pressure]
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diastolic blood pressure [GWAS:Hemostatic factors and hematological phenotypes]
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23andMe blog blood pressure [GWAS:Systolic blood pressure]
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diastolic blood pressure [PharmGKB:Non-Curated GWAS results: Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness (Initial Sample Size: 644-1,327 individuals, depending on measure (Framingham); Replication Sample Size: NR). This variant is associated with Blood pressure.] [GWAS:Blood pressure]
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rs5911874 associated with both nighttime and daytime diastolic and systolic blood pressure
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23andMe blog blood pressure [GWAS:Diastolic Blood Pressure]
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[GWAS:Blood pressure]
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[GWAS:Systolic blood pressure]
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[GWAS:Blood pressure]
Frequency: 64.6%
References:2
References:2
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systolic blood pressure [PharmGKB:Non-Curated GWAS results: Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness (Initial Sample Size: 644-1,327 individuals, depending on measure (Framingham); Replication Sample Size: NR). This variant is associated with Blood pressure.] [GWAS:Blood pressure]
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[GWAS:Blood pressure]
Frequency: 92.0%
References:1
References:1
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[GWAS:Blood pressure]
Frequency: 95.6%
References:1
References:1
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[GWAS:Blood pressure]
Frequency: 100.0%
References:1
References:1
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[GWAS:Blood pressure]
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This SNP, rs653178, is basically a proxy (r<sup>2</sup>>0.99) for rs3184504, as both are associated with celiac disease; see rs3184504 for more details. This SNP is also associated with risk of hypertension. 23andMe blog blood pressure [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 13; CELIAC13] [GWAS:Celiac disease]
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[GWAS:Blood pressure]
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23andMe blog blood pressure [GWAS:Systolic blood pressure]
Magnitude: 0
Frequency: 59.3%
Repute:Good
References:3
Frequency: 59.3%
Repute:Good
References:3
Magnitude: 0
Frequency: 69.0%
References:8
Frequency: 69.0%
References:8
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Each G allele is associated with 0.89 x odds of high blood pressure, according to 23andMe. 23andMe blog blood pressure High Blood Pressure (Hypertension) [GWAS:Systolic blood pressure]
common in complete genomics
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23andMe blog blood pressure [GWAS:Diastolic Blood Pressure]
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23andMe blog blood pressure Common variants in or near FGF5, CYP17A1 and MTHFR genes are associated with blood pressure and hypertension in Chinese Hans. [GWAS:Systolic blood pressure]
Magnitude: 0
Frequency: 85.8%
References:13
Frequency: 85.8%
References:13
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23andMe blog blood pressure [GWAS:Systolic blood pressure]
Magnitude: 0
Frequency: 85.8%
References:4
Frequency: 85.8%
References:4
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Based on a large study (~6,000 cases and 14,000 controls) of both European and Japanese populations, the rs12413409(G) allele has been associated with higher risk of aneurysm, with an odds ratio per allele of 1.29 (CI:1.19-1.40, p=1.2e-09). Also: 23andMe blog blood pressure Coronary Heart Disease High Blood Pressure (Hypertension) [OMIM:?] [GWAS:None]
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:0
Frequency: 85.8%
Repute:Good
References:0
normal
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A study of ~15,000 Europeans found that increased circulating natriuretic peptide and thus lower blood pressure and hypertension were associated with SNPs rs17376328(A), rs5068, rs198358(C), rs632793(G) 23andMe blog
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A study of ~15,000 Europeans found that increased circulating natriuretic peptide and thus lower blood pressure and hypertension were associated with SNPs rs17376328(A), rs5068, rs198358(C), rs632793(G) 23andMe blog
common in complete genomics
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Significant association was found between rs1055419 and diastolic blood pressure (OR = 0.53; p = 0.01) in a study of 962 obese individuals.
46 snps
(hide) Bloom syndrome
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Bloom syndrome see rs113993962
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
3 snps
(hide) Breast cancer
Lower lung cancer and increased breast cancer risk '''rs664677''' polymorphism was associated with decreased lung cancer risk and increased breast cancer risk (for lung cancer: TC vs. TT: OR = 0.76, 95% CI 0.62-0.92, CC vs. TT: OR = 0.80, 95% CI 0.64-0.99 and for breast cancer: TC vs. TT: OR = 1.42, 95% CI 1.17-1.73, CC vs. TT: OR = 1.51, 95% CI 1.21-1.87).
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Haplotype and linkage disequilibrium architecture for human cancer-associated genes. Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes. Explorative study to identify novel candidate genes related to oxaliplatin efficacy and toxicity using a DNA repair array. ATM polymorphisms and risk of lung cancer among never smokers.
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
Magnitude: 2
Frequency: 30.1%
Repute:Bad
References:106
Frequency: 30.1%
Repute:Bad
References:106
1.3x increased type-2 diabetes risk
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This SNP is in the TCF7L2 gene, and has been linked to type-2 diabetes, breast cancer and aggressive prostate cancer. This SNP is also known as IVS4G>T. is the paper which links it to Breast cancer. It suggests the T allele as increasing risk. reports the association of rs12255372 and rs7903146 with Type-2 diabetes in a Finnish sample. rs12255372 Common variants (rs12255372 and rs7903146) in TCF7L2 seem to be associated with an increased risk of diabetes among persons with impaired glucose tolerance Considered for type-2 diabetes with rs7903146 rs12255372 rs10885406. Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion as measured by acute insulin response and adjusted for the degree of insulin sensitivity (p = 0.036). In a study of 1,457 prostate cancer case...
slightly increased risk for breast cancer
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This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For this particular SNP, the risk (minor) allele is (G). For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry or BRCA1 and BRCA2.
Magnitude: 2
Frequency: 50.0%
Repute:Bad
References:77
Frequency: 50.0%
Repute:Bad
References:77
1.3x risk for Heart Attack. Normal risk for Abdominal Aortic Aneurysm and Brain Aneurysm. One copy of an SNP that increases risk of Myocardial Infarction (Heart Attack) and other Coronary Heart Disease. It has been shown that regularly eating raw vegetables and fruit can reduce the risk to the same level as people without this SNP. This SNP also has the normal medium risk of abdominal aortic aneurysm (weakened artery to abdomen and legs) or brain aneurysm (weakened artery to brain).
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This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...
Fast Caffeine Metabolizer. Unlike the majority of people, caffeine is broken down faster in your liver, so it has less effect on you. Supposedly this decreases heart attack risk, although other studies show caffeine is generally good for the heart. Caffeine will be less effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Caffeine will not make your breasts smaller.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Magnitude: 2
Frequency: 72.3%
Repute:Good
References:7
Frequency: 72.3%
Repute:Good
References:7
24% chance (lower than average) of docetaxel-induced leukopenia/neutropenia
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rs12762549 and rs11045585 can be used to predict whether docetaxel will induce leukopenia/neutropenia, according to a study of ~100 Japanese patients. When patients were classified into three groups by the scoring system based on the genotypes of these two SNPs, patients with a score of 1 or 2 were shown to have a significantly higher risk of docetaxel-induced leukopenia/neutropenia as compared to those with a score of 0 (P = 0.0000057; odds ratio [OR], 7.00; 95% CI [confidence interval], 2.95-16.59). This prediction system correctly classified 69.2% of severe leukopenia/neutropenia and 75.7% of non-leukopenia/neutropenia into the respective categories. [Effect percentages provided in table are raw population fractions taken from the referenced study based on rs11045585 only. Total populat...
Magnitude: 2
Frequency: 75.9%
References:12
Frequency: 75.9%
References:12
Wet earwax. Normal body odour. Normal colostrum. This is normal for non-Asians. It makes ear-wax wet, sticky, and honey-coloured. It also produces colostrum for breast feeding. People with this gene need to use deodorant to avoid smelling bad, unlike some Asians.
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rs17822931, also known as c.538G>A or G180R, is a SNP in the ATP-binding cassette, sub-family C (CFTR/MRP), member 11 ABCC11 gene. The ABCC11 protein helps transport small molecules across apical membranes such as those in apocrine secretory cells. This SNP determines wet vs dry earwax as well as sweat production, and it is also associated with lipid secretion. It is commonly (T;T) for Asians and (C;C) for Europeans and Africans. A study of deodorant usage in a large (17,000+) population showed that rs17822931(T;T) individuals were at least 5-fold less likely to use deodorant, consistent with them being 'genotypically nonodorous'. Although not statistically significant, there was some evidence for a heterozygote effect, implying that individuals with a (C;C) genotype for this SNP were l...
Magnitude: 1.6
Frequency: 7.9%
Repute:Bad
References:1
Frequency: 7.9%
Repute:Bad
References:1
>1.6x increased breast cancer risk for women over 60
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rs11523871, also known as 124A>C or Thr42Pro, is a SNP in the Deleted in Malignant Brain Tumors 1 DMBT1 gene. For more information about increased breast cancer risk for this SNP, see the SNPedia entry for rs2981745, to which it is tightly linked.
>1.6x increased risk for breast cancer in females over 60
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rs2981745, also known as -93C>T, is a SNP in a gene known as Deleted in Malignant Brain Tumors 1 DMBT1. The (overly descriptive?) name refers to the hypothesis that this gene has a role as a tumor suppressor. A study of 1,195 BRCA1/2 mutation negative German breast cancer families and 1,466 unrelated German controls concluded that rs2981745(T) carriers over the age of 60 are at increased risk for breast cancer, with an odds ratio of 1.66 (CI: 1.21-2.29, p=0.0017). rs2981745 was also said to be tightly linked to rs11523871, which showed the same odds ratios in this study.
1.4x increased risk for breast cancer
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rs1126497, also known as Thr115Met, is a SNP in the epithelial cell adhesion molecule EPCAM gene. In a study of case control study of 1643 individuals with breast cancer and 1818 control subjects in Eastern and Southern Chinese populations, the rs1126497(T) allele was associated with a 1.4x increased risk (CI: 1.16-1.57), and it was also associated with early breast cancer onset (p=0.0023). Functional polymorphism in the EpCAM gene is associated with occurrence and advanced disease status of cervical cancer in Chinese population.
0.75x (reduced) risk for metastasis in LN-/ER+ breast cancer patients
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rs9306160, also known as Pro436Leu, is a SNP in the ribosomal RNA processing 1 homolog B RRP1B gene. In a study of 1,725 LN=/ER+ breast cancer patients, carriers of a rs9306160(T) allele showed a reduced metastasis risk compared to rs9306160(C;C) patients. This association was statistically significant for both disease-free survival (DFS) and metastasis-free survival (MFS) in multivariate analysis [DFS hazard ratio 0.75, CI: 0.60–0.94, p=0.013), MFS HR 0.70, CI: 0.54–0.91, p=0.009) and overall survival (HR 0.78, CI:0.59–1.03, p=0.082)]. This study also found that rs9306160 can be combined with an independent predictor of metastasis free survival, rs2448490, to yield an even stronger prognostic. Specifically, the risk for developing distant metastasis was about 2.5-fold lo...
1.3x higher risk for endometrial cancer (in Chinese women)
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Category:interestingrs34330 shows an association with breast cancer in a British study involving ~2300 patients. The odds ratio for the (T;T) vs (C;C) homozygotes is 1.22 (CI: 1.02-1.47, p=0.013). found a significant association between rs34330 (-79C/T) and prostate cancer found higher odds for endometrial cancer among 1,200+ Chinese patients associated with rs34330, with an odds ratio of 1.33 (CI: 1.06-1.66) and 1.51 (CI: 1.16-1.94) for the (C;T) and (T;T) genotypes, respectively, compared with the (C;C) genotype. see also omim 176807 [OMIM:CYCLIN-DEPENDENT KINASE INHIBITOR 1B; CDKN1B] [GWAS:Systemic lupus erythematosus]
slight if any increased risk of Breast Cancer
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rs249954, also known as 2586+58C>T, is an intronic SNP in the PALB2 gene. There is conflicting literature about the association of this SNP with increased risk for breast cancer, but overall, it seems as if any association between rs249954 and breast cancer is likely to be either nonexistent or at least fairly small. Specifically: * ClinVar tags this SNP as benign, based on a single submission * A 2008 study of 1,000 Chinese with breast cancer reports a 36% increase in breast cancer risk (odds ratio 1.36, CI: 1.13-1.64, p = 0.001; TT/TC versus CC genotypes) * A 2010 study of 660 Chinese patients did not find an association for this SNP * A 2010 study of Polish patients reported an allele frequency of 5.7% (4 out of 70) in those patients but did not report the frequency in matched contro...
complex! see rs4880
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The rs4880(T) allele, part of the codon for amino acid valine at codon 16 of the antioxidant protein from the mitochrondrial superoxide dismutase 2 SOD2 gene, is the most common in most populations studied. The rs4880(C) allele gives rise to an alanine at this position is it also known as Val16Ala manganese superoxide dismutase, or A16V. There appears to be some conflict in the literature over the effect of this SNP. Having a valine at codon 16 is said to reduce enzyme activity , and thus lead to increased oxidative stress, yet in at least one study of the actual enzyme levels measured in people, SOD2 activity was 33% higher in (C;T) or (T;T) individuals compared to (C;C) individuals . Regardless of how this resolves, several phenotypic associations have been reported for this SNP, includi...
Very slightly higher risk for breast cancer
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rs889312 is a SNP near the MAP3K1 gene. rs889312 was one of the four strongest associating SNPs found in a genome-wide association study of over 4,000 breast cancer samples. . From a DeCode user report, it appears that the risk allele is C; this A;A individual reportedly has 0.93x risk of breast cancer. In a study of 1,267 breast cancer patients, rs889312 heterozygotes and minor allele homozygotes were less likely to be lymph node positive at breast cancer diagnosis (P = 0.044) relative to major allele homozygote carriers. A meta-analysis including 26,015 cases and 33,962 controls concludes that the rs889312(C) allele is clearly a significant - but quite weak - contributor to increased risk for breast cancer. breast cancer *rs2981582, rs3803662, and rs889312) showed weak but significant as...
Magnitude: 1.1
Frequency: 48.7%
Repute:Bad
References:40
Frequency: 48.7%
Repute:Bad
References:40
1.12x increased risk for breast cancer
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rs13387042(A;A) has an estimated 1.44-fold greater risk of breast cancer than the GG genotype. This initial association was later tested among patients in the Breast Cancer Association Consortium, including 31,510 women with invasive breast cancer, 1101 women with ductal carcinoma in situ (DCIS), and 35,969 controls. In Caucasian women of European origin, each A allele is associated with 1.12 higher odds (CI: 1.09-1.15). This association held regardless of ER or PR status. [PharmGKB:Non-Curated GWAS results: A multistage genome-wide association study in Breast Cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). (Initial Sample Size: 1,145 cases, 1,142 controls; Replication Sample Size: 8,625 cases, 9,657 controls); (Region: 2q35; Reported Gene(s): Intergenic; Risk Alle...
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Formerly known as the very well studied rs1982073 [PharmGKB:Curated In conjunction with polymorphism at codon 25, defines high-, medium- or low-producer haplotype; Pro allele has been associated with higher levels of circulating TGFB1; Cystic Fibrosis patients who are C homozygotes may have increased risk of severe pulmonary disease; association found of C allele with increased risk of invasive breast cancer; associated with bone mineral density and genetic susceptibility to osteoporosis in Japanese adolescents and postmenopausal women; C allele may be involved in development of EBV-related diseases;C allele associated with increased risk for esophageal squamous cell carcinoma in Chinese; T allele associated with familial vesicoureteral reflux; C allele associated with increased severity ...
Frequency: 1.8%
References:7
References:7
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23andMe blog each copy of an A at rs10995190 was associated with a 2% decrease in mammographic density. The researchers also found that each copy of an A at rs10995190 is also associated with slightly lower odds of developing breast cancer Breast Cancer Risk Modifiers [GWAS:Breast cancer]
Frequency: 2.7%
References:1
References:1
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[GWAS:Breast cancer]
0.42x reduced lymphoma risk
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Associated with (reduced) risk for follicular lymphoma. Based on studying ~1,300 patients in 2 populations, for (C;C) homozygotes, the odds ratio was 0.42 (CI: 0.23-0.77), and for the (C;T) heterozygotes, 0.64 (CI: .46-.88), p(trend) = 4x10e-4. estrogen receptor-positive breast cancer risk (C) have an Odds Ratio (OR) = 1.05 [95% Confidence Intervals (CI) 1.02-1.09] relative to t-allele homozygotes, P= 0.004. [PharmGKB:Curated In a French study population, the C allele of this SNP, which is located in intron 4 of ESR1, was associated with increased incidence of type 2 diabetes (diabetes mellitus, type 2). The C allele of this SNP was associated with increased fasting plasma glucose levels in Swedish males, although there was no significant association in the Swedish cohort between this SNP...
Frequency: 12.4%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: A pilot genome-wide association study of early-onset breast cancer (Initial Sample Size: 30 cases, 30 controls; Replication Sample Size: NR). This variant is associated with Breast cancer.] [GWAS:Breast cancer]
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[OMIM:?] [GWAS:Breast cancer]
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[PharmGKB:Non-Curated GWAS results: A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study (Initial Sample Size: 1,345 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Breast cancer.] [GWAS:Breast cancer]
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Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. Breast cancer susceptibility loci and mammographic density. Breast cancer risk polymorphisms and interaction with ionizing radiation among U.S. radiologic technologists. Association between breast cancer susceptibility loci and mammographic density: the Multiethnic Cohort. Association between invasive ovarian cancer susceptibility and 11 best candidate SNPs from breast cancer genome-wide association study. Correcting 'winner's curse' in odds ratios from genomewide association findings for major complex human diseases. Gene-environment interactions in 7610 women with breast cancer: prospective evidence from the Million Women Study. Combined effect of low-penetrant SNPs on breast cancer risk. [GWAS:Br...
Frequency: 19.5%
References:1
References:1
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[GWAS:Breast cancer]
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[GWAS:Breast cancer]
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breast cancer http://www.nature.com/ng/journal/v42/n10/full/ng.669.html This SNP is associated with risk of breast cancer. [GWAS:None]
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[GWAS:Breast cancer]
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in Chinese women no significant breast cancer association at rs1011970, rs10757278 or rs2380205 [GWAS:Breast cancer]
Frequency: 24.8%
References:0
References:0
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breast cancer, GWAS<br> Nature Genetics:
Frequency: 25.7%
References:4
References:4
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[PharmGKB:Non-Curated GWAS results: A multistage genome-wide association study in Breast Cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). (Initial Sample Size: 1,145 cases, 1,142 controls; Replication Sample Size: 8,625 cases, 9,657 controls); (Region: 5q11.2; Reported Gene(s): MAP3K1; Risk Allele: rs16886165-G); (p-value= 0.0000005).This variant is associated with Breast Cancer.] [GWAS:Breast cancer]
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rs249954 and rs120963 were associated with an increase of breast cancer risk in a Chinese population.
normal
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rs2981578 is a SNP within intron 2 of the FGFR2 gene, as part of a haplotype associated with increased risk for sporadic postmenopausal ER+ breast cancer in Caucasian patients. The risk shown for this SNP is actually the risk calculated for the tightly associated SNP rs1219648. The distinguishing feature of rs2981578 is experimental evidence indicating that it is one of two SNPs in this intron that appear to have a (the?) functional role associated with the transcriptional regulation of the FGFR2 gene. The minor alleles of both SNPs, rs2981578 and rs7895676, lead to increased transcription and increased breast cancer risk. Common variation in the fibroblast growth factor receptor 2 gene is not associated with endometriosis risk. Allele-specific up-regulation of FGFR2 increases susceptibili...
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[PharmGKB:Non-Curated GWAS results: A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study (Initial Sample Size: 1,345 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Breast cancer.] [GWAS:Breast cancer]
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rs2470152 is clearly associated with serum E2 and E1 levels in men, influencing risk of many conditions including prostate cancer, breast cancer and osteoporosis
Frequency: 31.2%
References:3
References:3
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[GWAS:Breast cancer]
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[GWAS:Breast cancer]
Frequency: 33.0%
References:7
References:7
common
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This SNP is basically a proxy for SNP rs1219648, which represents the SNP in the FGFR2 gene with the strongest association with breast cancer.
normal
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Based on a mixed-ethnicity study, women consuming a diet high in linoleic acid (top quartile of intake, >17.4 g/d) and carrying the rs4076128(A;A) genotype were associated with higher breast cancer risk (age- and race-adjusted odds ratio, 1.8, CI: 1.2-2.9) compared with (A;G) and (G;G) genotypes. Among women consuming </=17.4 g/d of linoleic acid, there was no association with breast cancer risk.
common
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This SNP is basically a proxy for SNP rs1219648, which represents the SNP in the FGFR2 gene with the strongest association with breast cancer. {Note: the alleles shown for this SNP in SNPedia are in orientation to the dbSNP entry, not as published.] Common variation in the fibroblast growth factor receptor 2 gene is not associated with endometriosis risk. Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. Histone-acetylated control of fibroblast growth factor receptor 2 intron 2 polymorphisms and isoform splicing in breast cancer. Genetic variants in FGFR2 and FGFR4 genes and skin cancer risk in the Nurses' Health Study. FGFR2 and other loci identified in genome-wide association studies are associated with breast cancer in African-American and younge...
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[GWAS:Breast cancer]
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[GWAS:Breast cancer]
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[GWAS:Breast cancer]
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[OMIM:?] [GWAS:Breast cancer]
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Associated with periodontitis in a study of Chinese patients. rs2228570 aka rs10735810 allele (A) observed for breast cancer odds ratio (OR) of 1.26 Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. Variants in the vitamin D receptor gene and asthma. Gene-environment interaction effects on the development of immune responses in the 1st year of life. Vitamin D receptor polymorphisms are associated with Graves' disease in German and Polish but not in Serbian patients. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Polymorphisms in the ...
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DeCode reports that rs7222197 in the COX11 gene is associated with risk of breast cancer.
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[GWAS:Breast cancer]
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breast cancer, GWAS<br> Nature Genetics:
Frequency: 38.9%
References:3
References:3
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[GWAS:Breast size]
slightly reduced breast cancer odds?
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A study of 300 breast cancer cases in Germany concluded that the rs1467465(C) allele might have some protective effect.
normal
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A study of 733 breast cancer cases for 10 SNPs concluded that the rs1501299(C;C) genotype (in dbSNP orientation) was at increased risk (odds ratio 1.80, CI: 1.14 - 2.85). After categorizing individuals by adiponectin signaling status, this study found that compared with high signalers, intermediate signalers had a 4.16-fold increase in breast cancer risk (CI: 0.49-35.19), and low signalers had a 6.56x higher breast cancer risk (CI: 0.78-54.89, p(trend) = 0.001). Adiponectin signaling status was assigned as follows: rs1501299(G,G) + rs2241766(T,T) = low signaler<br> rs1501299(G,T) + rs2241766(T,T) = low signaler<br> rs1501299(G,G) + rs2241766(G,T) = low signaler<br> rs1501299(T,T) + rs2241766(T,T) = intermediate signaler<br> rs1501299(G,T) + rs2241766(G,T) = intermed...
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[GWAS:Breast cancer]
Frequency: 40.2%
References:1
References:1
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[GWAS:Breast cancer]
1.16x increased risk for breast cancer
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breast cancer rs1061646 was associated with risk in the initial study (p=0.0052), and in the replication studies (p=0.032). In a combined analysis, (8,556 cases, 9,605 controls) this SNP yielded an 8% increase in risk per allele. Note that this analysis was carried out in a multi-ethnic study, and rs1061646 showed more consistent association with risk in non-Caucasian populations.
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A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). [GWAS:Breast cancer]
Frequency: 41.6%
References:2
References:2
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[GWAS:Breast cancer]
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breast cancer rs6503691 rs7211777 Carriers of the AC haplotype, which represents the variant alleles of both SNPs, were at an increased risk (OR = 1.41, 95% CI 1.09-1.82). A decreased risk was observed for carriers of the AT haplotype (OR = 0.60, 95% CI 0.38-0.94). Furthermore, individuals with the AC/GC diplotype were at a significantly increased risk (OR = 1.88, 95% CI 1.13-3.14)
Frequency: 42.0%
References:14
References:14
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Chinese breast cancer rs11568818(G;G) significantly worse prognosis (OS HR: 6.7, 95% CI: 2.4-18.6) than patients homozygous for the common allele (A) [GWAS:Prostate cancer]
0.59x decreased breast cancer risk
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A study of 733 breast cancer cases for 10 SNPs concluded that a rs7539542 genotype was associated with decreased risk (odds ratio 0.51, CI: 0.28-0.92). After categorizing individuals by adiponectin signaling status, this study found that compared with high signalers, intermediate signalers had a 4.16-fold increase in breast cancer risk (CI: 0.49-35.19), and low signalers had a 6.56x higher breast cancer risk (CI: 0.78-54.89, p(trend) = 0.001). Adiponectin signaling status was assigned as follows: rs1501299(G,G) + rs2241766(T,T) = low signaler<br> rs1501299(G,T) + rs2241766(T,T) = low signaler<br> rs1501299(G,G) + rs2241766(G,T) = low signaler<br> rs1501299(T,T) + rs2241766(T,T) = intermediate signaler<br> rs1501299(G,T) + rs2241766(G,T) = intermediate signaler<br...
Frequency: 42.5%
References:1
References:1
normal
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rs10801935 is a SNP in the V-set domain containing T cell activation inhibitor 1 VTCN1 gene, which is also known as B7-H4. A study of 500 Chinese Han women with breast cancer (and an equal number of matched controls) concluded that the rs10801935(C;C) genotype showed a significantly decreased risk of breast cancer (odds ratio 0.328, CI: 0.145-0.739).
Frequency: 42.5%
References:4
References:4
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breast cancer 1,134 breast cancer patients recruited as part of the Shanghai Breast Cancer Study who were followed for a median of 7.1 years. rs16949649(C) associated with higher breast cancer-specific mortality [hazard ratio (HR), 1.4; 95% confidence interval (95% CI), 1.1-1.9]
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increased risk of breast cancer with concurrent proliferative fibrocystic conditions *rs1004982(C) 2.19 (1.24-3.85) *rs28566535(C) 2.20 (1.27-3.82) *rs936306(T) 1.94 (1.13-3.30) *rs4775936(C) 1.95 (1.07-3.58) A new SNP in a negative regulatory region of the CYP19A1 gene is associated with lumbar spine BMD in postmenopausal women. Genome-wide association with bone mass and geometry in the Framingham Heart Study. Polymorphisms in the estrogen receptor 1 and vitamin C and matrix metalloproteinase gene families are associated with susceptibility to lymphoma. Quantitative trait loci, genes, and polymorphisms that regulate bone mineral density in mouse. [OMIM:CYTOCHROME P450, FAMILY 19, SUBFAMILY A, POLYPEPTIDE 1; CYP19A1]
0.78x reduced risk for breast cancer
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rs3750817 is a SNP in the fibroblast growth factor receptor 2 FGFR2 gene. A study of 2,166 invasive breast cancer cases concluded that carriers of a rs3750817(T) allele had lower risk for cancer, with an estimated per-minor-allele odds ratio of 0.78. Success with hormone therapy to treat postmenopausal symptoms also correlated with the number of rs3750817(T) alleles. Common variation in the fibroblast growth factor receptor 2 gene is not associated with endometriosis risk. [GWAS:Breast cancer]
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NIH rs999737 is located near an interesting gene, RAD51L1, which is in a pathway previously implicated in breast cancer risk. The protein encoded by this gene interacts directly with those of other genes that are involved in DNA repair and in the exchange of material between strands of DNA. common variants at 14q24.1 might not be associated with the risk of breast cancer in the Chinese population. Rs999737 is not a risk allele for Chinese [PharmGKB:Non-Curated GWAS results: A multistage genome-wide association study in Breast Cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). (Initial Sample Size: 1,145 cases, 1,142 controls; Replication Sample Size: 8,625 cases, 9,657 controls); (Region: 14q24.1; Reported Gene(s): RAD51L1; Risk Allele: rs999737-C); (p-value= 0.000000...
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
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rs3817198 is a SNP in the LSP1 gene on chromosome 11. The less frequent allele rs3817198(C) increases risk of breast cancer by about +10% in Caucasians, but actually may be protective in women of African ancestry. rs3817198, a SNP associated with the LSP1 gene, was one of the four strongest associating SNPs found in a genome-wide association study of over 4,000 breast cancer samples. [PharmGKB:Non-Curated GWAS Results: Genome-wide association study identifies novel breast cancer susceptibility loci (Initial Sample Size: 390 cases, 364 controls; Replication Sample Size: 26,646 cases, 24,889 controls; Risk Allele: rs3817198-T).] [OMIM:BRCA2 GENE; BRCA2] [GWAS:Breast cancer] [GWAS:Breast cancer]
Frequency: 44.6%
References:55
References:55
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breast cancer *rs13281615 in 8q24 was stronger for ER-positive, PR-positive, and low grade tumors (P = 0.001, 0.011 and 10(-4), respectively) and improvement in survival after diagnosis (per-allele HR = 0.90 (0.83-0.97). rs13281615 confirmed in 988 sporadic breast cancer cases and 1,016 controls from the West of Ireland to be associated with increased risk (odds ratio 1.17, p(allelic) = 1.8 x 10e-2) for breast cancer [PharmGKB:Non-Curated GWAS Results: Genome-wide association study identifies novel breast cancer susceptibility loci (Initial Sample Size: 390 cases, 364 controls; Replication Sample Size: 26,646 cases, 24,889 controls; Risk Allele: rs13281615-T).] [OMIM:BREAST CANCER] [GWAS:Breast cancer] [GWAS:Breast cancer]
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possible association with breast cancer
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[GWAS:Breast cancer]
Frequency: 46.0%
References:17
References:17
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[GWAS:None]
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[GWAS:Breast cancer]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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cancer-genetics these snps influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 rs7931342 showed some evidence of association with breast cancer (per minor allele OR, 0.95; 95% CI, 0.91-0.99; P(trend) = 0.028) Multiple novel prostate cancer predisposition loci confirmed by an international study: the PRACTICAL Consortium. Prostate cancer genomics: towards a new understanding. Generalizability of associations from prostate cancer genome-wide association studies in multiple populations. Analysis of recently identified prostate cancer susceptibility loci in a population-based study: associations with family history and clinical features. Two indepe...
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This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
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rs2380165, rs2412546 and rs4417527 associated with breast cancer
normal
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rs1131532 is a SNP in the tumor necrosis factor superfamily member 10 TNFSF10 gene. A study of 240 patients with early invasive ductal breast cancer followed for a median of 53 months concluded that rs1131532(T;T) individuals had lower odds of being disease-free or distant-disease free, and for overall survival (hazard ratio 3.304, 4.757, and 6.459; p = 0.002, 0.001, and 0.009, respectively).
poorer survival rate if breast cancer patient
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rs438034 is a SNP in the centromere protein F CENPF gene. Based on a long-term (up to 15 years) study of 749 Swedish women with breast cancer, carriers of rs438034(T) alleles (as oriented wrt dbSNP) had poorer specific survival rates as compared to rs438034(C;C) individuals. The hazard ratio was 2.65 (CI: 1.19-5.90). However, although rs438034(T) carriers had worse survival odds, they were less likely to have either regional lymph node metastases (odds ratio 0.71, CI: 0.51-1.01) or tumors of stage II-IV (OR 0.73, CI 0.54-0.99). [GWAS:None]
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[GWAS:Breast cancer]
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possible association with breast cancer
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rs1047840, also known as K589E, is a SNP in the EXO1 gene. A study of 1,272 breast cancer Taiwanese patients concluded that the rs1047840(A) allele conferred a significantly (p=0.000025) increased risk of breast cancer.
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[GWAS:Breast cancer]
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rs4415084 and rs10941679 confer risk for estrogen receptor breast cancer (ER)-positive tumors (OR = 1.27, P = 2.5E-12 for rs10941679) based on a study of 6,145 cases. From a DeCode user report, the risk allele appears to be T; this T;T individual reportedly has a 1.19x increased risk of breast cancer. the two risk SNPs reported in the European population were neither associated with breast cancer risk in our Chinese population A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Leveraging genetic variability across populations for the identification of causal variants. [PharmGKB:Curated This variant is associated with risk for estrogen receptor (ER)-positive breast cancer.] [OMIM:BREAST CANCER] [GWAS:None]
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cancergenetics The risk of breast cancer was 23% higher in women who had one copy of genetic variant (the A-C-A haplotype: rs7712023-rs299290-rs10515860), and 46% higher in women with two copies. In addition, those women were diagnosed an average of 12 months younger than women from the control group, suggesting that HMMR is linked to early-onset breast cancer. However, a more recent, larger European case-control study found no association between rs299290 and risk of breast cancer. breast cancer *rs10515860 [odds ratio (OR; AA/GG), 0.85; 95% confidence interval (CI), 0.65-1.12; P(trend) = 0.9], *rs299290 [OR (CC/TT), 1.00; 95% CI, 0.87-1.15; P(trend) = 0.7], *rs3756648 (rs7712023) [OR (TT/CC), 0.93; 95% CI, 0.84-1.02; P(trend) = 0.1], *rs299284 [OR (TT/CC), 1.01; 95% CI, 0.76-1.35; P(tren...
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Genetic variants at chromosome 9p21, 10p15 and 10q22 and breast cancer susceptibility in a Chinese population. four common SNPs at 9p21(rs1011970 and rs10757278), 10p15 (rs2380205), and 10q22 (rs1250009) in a two-stage case-control study with a total of 1792 breast cancer cases and 1,867 controls. We found that rs1250009 at 10q22 was consistently associated with risk of breast cancer in stage 1 and stage 2, with a per-allele OR of 1.13 (95% CI 1.02-1.25) after two stages combined (P = 0.023). However, no significant associations were observed between the other three SNPs and breast cancer risk. in Chinese women no significant breast cancer association at rs1011970, rs10757278 or rs2380205 [GWAS:Breast cancer]
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increased risk of breast cancer with concurrent proliferative fibrocystic conditions *rs1004982(C) 2.19 (1.24-3.85) *rs28566535(C) 2.20 (1.27-3.82) *rs936306(T) 1.94 (1.13-3.30) *rs4775936(C) 1.95 (1.07-3.58)
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breast cancer *rs10515860 [odds ratio (OR; AA/GG), 0.85; 95% confidence interval (CI), 0.65-1.12; P(trend) = 0.9], *rs299290 [OR (CC/TT), 1.00; 95% CI, 0.87-1.15; P(trend) = 0.7], *rs3756648 (rs7712023) [OR (TT/CC), 0.93; 95% CI, 0.84-1.02; P(trend) = 0.1], *rs299284 [OR (TT/CC), 1.01; 95% CI, 0.76-1.35; P(trend) = 0.5], and *rs13183712 [OR (TT/GG), 1.04; 95% CI, 0.88-1.23; P(trend) = 0.6].
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rs997669 shows an association with breast cancer in a British study involving ~2300 patients. The odds ratio for the (G;G) vs (A;A) homozygotes is 1.18 (CI: 1.04-1.34, p=0.003).
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[GWAS:Breast cancer]
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rs2380165, rs2412546 and rs4417527 associated with breast cancer
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[GWAS:Breast cancer]
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the rare allele of rs2191249 is associated with a poorer prognosis (hazard ratio per minor allele, 1.20; 95% CI, 1.07-1.36; P trend = 0.002) for breast cancer
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[PharmGKB:Non-Curated GWAS Results: Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33 (Initial Sample Size: 249 cases, 299 controls (Ashkenazi Jewish, non-BRCA1/2 carriers); Replication Sample Size: 1,193 cases, 1,166 controls (Ashkenazi Jewish, non-BRCA1/2 carriers); Risk Allele: rs2180341-G).] [GWAS:Breast cancer]
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[GWAS:Breast cancer]
In women diagnosed with breast cancer, this genotype is less favorable. It is more associated with lymph node metastasis
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PMID: 16563182 This SNP in can have implications for prognosis in breast cancer. It is located 313 base pairs upstream of the 5'-untranslated region of SIPA1 and is considered to be within the promoter region of the gene. SIPA1 germline polymorphisms are associated with aggressive disease behavior(lymph node metastasis) in the cohort examined
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[GWAS:Breast cancer]
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rs4646(A) allele carriers with breast cancer being treated with letrozole are reported to do worse than rs4646(C;C) patients, based on a study of (only) 95 women. [PharmGKB:Curated A study in 67 patients with hormone receptor-positive metastatic breast cancer treated with letrozole, the presence of this SNP in the 3' untranslated region of the CYP19A1 gene is associated with improved treatment efficacy.]
Frequency: 58.5%
References:17
References:17
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rs4415084 and rs10941679 confer risk for estrogen receptor breast cancer (ER)-positive tumors (OR = 1.27, P = 2.5E-12 for rs10941679) based on a study of 6,145 cases. Genetic susceptibility loci for breast cancer by estrogen receptor status. Association between breast cancer susceptibility loci and mammographic density: the Multiethnic Cohort. A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Risk of estrogen receptor-positive and -negative breast cancer and single-nucleotide polymorphism 2q35-rs13387042. Familial relative risks for breast cancer by pathological subtype: a population-based cohort study. Genetic and clinical predictors for breast cancer risk assessment and stratification among Chinese women. The role...
Frequency: 60.9%
References:1
References:1
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[GWAS:Breast cancer]
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[PharmGKB:Non-Curated GWAS results: A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study (Initial Sample Size: 1,345 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Breast cancer.] [GWAS:Breast cancer]
Frequency: 65.5%
References:1
References:1
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[GWAS:Breast cancer]
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Associated with Accelerated Bone Mineral Density Loss after Hematopoietic Cell Transplantation [PharmGKB:Non-Curated GWAS results: A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study (Initial Sample Size: 1,345 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Breast cancer.] [GWAS:Breast cancer]
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[GWAS:Breast cancer]
Frequency: 70.8%
References:6
References:6
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[GWAS:Breast Cancer in BRCA1 mutation carriers]
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[GWAS:Breast cancer]
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breast size [GWAS:Breast cancer]
Frequency: 81.2%
References:0
References:0
normal
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rs12184413(T;T) was associated with reduced risk for breast cancer, with an odds ratio of 0.7 (CI: 0.6-0.9), based on a study ultimately totaling over 3,000 cases (and an equal number of controls). Genetic polymorphisms in the MMP-7 gene and breast cancer survival. No association between matrix metalloproteinase (MMP)-1, MMP-3, and MMP-7 SNPs and endometrial cancer risk.
Frequency: 82.3%
References:11
References:11
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rs17887200 and rs12951053 associated with ER negative breast cancer tumors (1.48 (1.11-1.93) p-trend = 0.01 and 1.29 (1.06-1.58) p-trend = 0.009, respectively) A study population including a total of 5,206 invasive ovarian cancer cases (2,829 of which were serous) and 8,790 controls found an association between rs12951053 and serous invasive cancer (median per allele odds ratio 1.19, CI: 1.01-1.38).
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[GWAS:Breast cancer]
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rs3740065 is a SNP in the ATP-binding cassette, sub-family C (CFTR/MRP), member 2 ABCC2 gene. A study of 282 hormone receptor-positive, invasive breast cancer Japanese patients receiving tamoxifen found a significant association with shorter recurrence-free survival (p = .00017; hazard ratio 10.64, CI: 1.44 - 78.88) in rs3740065(T;T) patients; the hazard ratio for carriers of one (T) allele was 3.5 (CI: 0.5-26). Curiously, no significant difference in plasma levels of the tamoxifen metabolites endoxifen or 4-hydroxytamoxifen were seen. This same study of tamoxifen users concluded that rs3740065(T;T) patients who also had two CYP2D6 risk alleles had a 45 fold higher risk of recurrence than patients with zero or one (out of the possible four) risk alleles. The overall average recurrence risk...
Frequency: 90.3%
References:1
References:1
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[GWAS:Breast cancer]
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[GWAS:Breast cancer]
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breast cancer
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breast cancer
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breast cancer
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breast cancer
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breast cancer
References:14
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NIH Although the function of this SNP is unknown, further analysis by the CGEMS team found that this region is predominately associated with estrogen receptor-positive breast cancer. From one person's DeCode report, it appears that the risk allele is C (relative risk 1.18 with two copies; apparently this information comes from a study or studies involving 9,335 cases and 10,263 controls). no significant association was observed between rs11249433 and breast cancer risk in this Chinese population Leveraging genetic variability across populations for the identification of causal variants. Performance of common genetic variants in breast-cancer risk models. [PharmGKB:Non-Curated GWAS results: A multistage genome-wide association study in Breast Cancer identifies two new risk alleles at 1p11....
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rs1799750 is a relatively common SNP at position -1,607 of the promoter of the MMP1 gene, consisting of an insertion polymorphism. In general, the insertion genotype ('2G/2G') is reported to lead to higher transcriptional activity of this gene, leading potentially to higher levels or rates of collagen breakdown. In a study of ~200 breast cancer patients, those with rs1799750(G;G) genotype, i.e. also known as the '2G/2G' genotype, had increased frequency of lymph node metastasis and thus a poorer prognosis. The odds ratio for mixed ethnicities was 3.9 (CI: 1.7-9.4, p=0.001), and when calculated only for Caucasians, 2.6 (CI: 1.0-6.9, p=0.06). Subsequently, a 2012 meta-analysis based on about 10,000 cancer cases, half of which metastasized, concluded that 2G/2G genotypes had a slightly higher...
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Linked to breast cancer [OMIM:LONGEVITY, REDUCED]
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A study of 733 breast cancer cases for 10 SNPs concluded that the rs2241766(G;T) genotype, in combination with certain genotypes at rs1501299, was at reduced risk (odds ratio 0.61, CI: 0.46-0.80). After categorizing individuals by adiponectin signaling status, this study found that compared with high signalers, intermediate signalers had a 4.16-fold increase in breast cancer risk (CI: 0.49-35.19), and low signalers had a 6.56x higher breast cancer risk (CI: 0.78-54.89, p(trend) = 0.001). Adiponectin signaling status was assigned as follows: rs1501299(G,G) + rs2241766(T,T) = low signaler<br> rs1501299(G,T) + rs2241766(T,T) = low signaler<br> rs1501299(G,G) + rs2241766(G,T) = low signaler<br> rs1501299(T,T) + rs2241766(T,T) = intermediate signaler<br> rs1501299(G,T) +...
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798 invasive breast cancer cases and 843 unaffected controls *rs454886 per allele odds ratio, 1.23; 95% confidence intervals, 1.05-1.43; P(trend) = 0.01 [PharmGKB:Curated In 798 invasive breast cancer cases and 843 unaffected controls this SNP in the APC tumor suppressor gene was associated with increased breast cancer risk.] [OMIM:?]
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rs6257 is a potential breast cancer variant Ovarian cancer risk and common variation in the sex hormone-binding globulin gene: a population-based case-control study. Genetic polymorphisms are associated with serum levels of sex hormone binding globulin in postmenopausal women. Usefulness of Mendelian randomization in observational epidemiology. Coffee and caffeine consumption in relation to sex hormone-binding globulin and risk of type 2 diabetes in postmenopausal women. [OMIM:?]
References:0
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rs80359543, also known as 6076del4, c.5848_5851delGTTA and p.Val1950_Ser1951?fs, is a variant in the BRCA2 gene considered pathogenic for breast cancer in ClinVar.
References:0
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rs80359752, also known as 9481insA, c.9253_9254insA and p.Thr3085?fs, is a variant in the BRCA2 gene considered pathogenic for breast cancer in ClinVar.
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This SNP is associated with risk of breast cancer. MAST3: a novel IBD risk factor that modulates TLR4 signaling. Mutation screening of the MERIT40 gene encoding a novel BRCA1 and RAP80 interacting protein in breast cancer families. Common breast cancer susceptibility loci are associated with triple-negative breast cancer. Common variants at the 19p13.1 and ZNF365 loci are associated with ER subtypes of breast cancer and ovarian cancer risk in BRCA1 and BRCA2 mutation carriers. [GWAS:None]
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the presence of at least one G allele at rs1008805 was significantly associated with an increase in the risk of breast cancer (OR = 1.72 [95% CI, 1.20-2.49]), especially with estrogen and progesterone receptor negative breast cancer (OR = 3.89 [1.74-8.70] and OR = 2.52 [1.26-5.05], respectively).
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rs5277 is a SNP in the prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) PTGS2 gene, also known as COX-2. A meta-analysis involving nine studies with 6,968 breast cancer cases and 9,126 controls found just a borderline significant increased risk (of breast cancer) in a recessive model (odds ratio 1.217, CI: 0.958-1.547, p = 0.107). Cyclooxygenase-2 polymorphisms in Parkinson's disease. A polymorphism in the 3' untranslated region of the gene encoding prostaglandin endoperoxide synthase 2 is not associated with an increase in breast cancer risk: a nested case-control study. Lack of association of the cyclooxygenase-2 and inducible nitric oxide synthase gene polymorphism with risk of cervical cancer in Korean population. Polymorphic variants in PTGS2 and p...
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[PharmGKB:Non-Curated GWAS results: A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study (Initial Sample Size: 1,345 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Breast cancer.] [GWAS:Breast cancer]
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rs2380165, rs2412546 and rs4417527 associated with breast cancer
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rs1801320, also known as 135G>C, is a SNP in the 5'-untranslated region (UTR) of the RAD51 gene. A meta-analysis of 12 studies involving 7,065 cases and 6,981 controls found no evidence for a significant association between rs1801320 and risk for breast cancer in non-BRCA1/BRCA1 carriers, contrary to a previous report. rs1801320 in the CIMBA study so perhaps breast cancer related
1.25x higher risk for breast cancer
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rs3176336 shows an association with breast cancer in a British study involving ~2300 patients. The odds ratio for the (T;T) vs (A;A) homozygotes is 1.25 (CI: 1.11-1.42, p=0.0026).
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rs4151620(C;G) and rs4151620(G;G) are associated with a reduced risk of ovarian cancer compared with rs4151620(G;G) individuals. This snp has been linked to ovarian cancer Intron 17 of RB1 contains the open reading frame for the P2RY5 gene, and rs4151620 is perfectly correlated with rs2227311, which is located in the 5'-untranslated region of P2RY5 and is predicted to affect P2RY5 transcription. rs2854344 has been reported previously to be associated with breast cancer risk
Magnitude: 0
Frequency: 25.7%
References:17
Frequency: 25.7%
References:17
normal
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Within the FTO gene, many SNPs appear to be co-inherited. The SNP showing the strongest association with body weight (i.e. body mass index, BMI) is not rs17817449, although this SNP is one of co-inherited SNPs in the FTO gene region. For more information, refer to the FTO gene or the most studied of FTO SNPs, rs9930506. A study of 900+ Quebec individuals reported that rs17817449 was associated with BMI (p=0.0014), weight (p=0.0059) and waist circumference (p=0.0021) under an additive model, and in addition, influenced fasting insulin (p=0.011) and HOMA-IR (p=0.038). * Note: The three FTO SNPs, rs1421085, rs17817449, and rs9939609, are in strong linkage disequilibrium (pairwise r<sup>2</sup>>0.97), and there are two primary haplotypes, C-G-A (42.0 %) and T-T-T (55.5 %). This ...
normal asthma risk in certain populations
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common...
common
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This SNP is basically a proxy for SNP rs1219648, which represents the SNP in the FGFR2 gene with the strongest association with breast cancer. Based on a study of 1,049 Chinese breast cancer patients, carriers of risk alleles at three SNPs (rs2981582, rs1219648 and rs2420946) were at 1.36x increased risk for breast cancer (CI: 1.13-1.62, p = 0.001).
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Based on a study of ~2500 female patients of European ancestry with sporadic postmenopausal breast cancer, this SNP in the FGFR2 showed the greatest risk. The risk allele is rs1219648(G), with a pooled odds ratio of 1.64 (CI:1.42-1.90) for rs1219648(G;G) homozygotes, and an odds ratio of 1.20 (CI: 1.07-1.42) for rs1219648(A;G) heterozygotes, compared with rs1219648(A;A) homozygotes. rs1219648 represents the SNP in the FGFR2 gene with the strongest association with breast cancer. However, nearby SNPs are almost as predictive. In particular, the following SNP alleles all have linkage values of 0.96 or greater with the rs1219648(G) allele in European populations: *rs2981579(A) *rs2420946(T) *rs11200014(A) An experimental rationale is presented indicating that this SNP is part of a haplotype t...
normal
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rs2981582 in the FGFR2 gene was one of the four strongest associations found in a genome-wide association study (GWAS) of over 4,000 breast cancer samples. The T allele was more strongly related to ER-positive (per-allele odds ratio 1.31 (CI: 1.27-1.36)) than ER-negative (odds ratio 1.08 (CI:1.03-1.14)) disease (p for heterogeneity = 10(-13)). While on its own still of fairly small effect, this was the most significant of 7 SNPs to help estimate risk of breast cancer. Family history and/or BRCA1 or BRCA2 testing status are more significant factors, which were not part of this panel. Based on a study of 1,049 Chinese breast cancer patients, carriers of risk alleles at three SNPs (rs2981582, rs1219648 and rs2420946) were at 1.36x increased risk for breast cancer (CI: 1.13-1.62, p = 0.001). A...
normal risk
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rs3731239 shows a slight protective association against breast cancer in a British study involving ~2300 patients. The odds ratio for the (C;C) vs (T;T) homozygotes is 0.90 (CI: 0.79-1.03, p=0.013). ovarian cancer rs3731239 rs602652 rs3212879 rs649392 rs3212891 rs2069391, rs2069414 rs17528736 rs3218036
normal
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rs351855, a SNP in the fibroblast growth factor receptor 4 (FGFR4) gene, is also known as the Gly388Arg variant. The rs351855(T) allele encodes the risk (Arg) allele. The Arg form of this SNP is likely to cause a harder to treat version of node-positive breast cancer, including reducing the efficacy of Herceptin, based on a study of 372 patients. A study of ~500 Japanese prostate cancer patients found that individuals with a rs351855(T;T) genotype had a 2.2- and 1.9-fold increased risk of prostate cancer and benign prostate hyperplasia (BPH), and a 1.8-fold increased risk of metastatic prostate cancer compared to the (C;C) genotype. A meta-analysis published in 2011, surveying a total of 2,618 cases of prostate cancer, concluded that the odds ratio per rs351855(T) allele was 1.17 (CI: 1.07...
normal
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G), encoding the His; the SNP is also known as N372H or Asn372His. In a separate study, rs144848(G;G) homozygotes were determined to have a 1.31x increased risk (CI: 1.07-1.61) for breast cancer greater risk compared to (T;T) genotypes. Interestingly, in normal females of all ages there is a significant deficiency of homozygotes compared with that expected from Hardy-Weinberg equilibrium, whereas in males there...
normal
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rs1056836, also known as 4326C/G, Val432Leu or L432V, is a SNP in the cytochrome P450 1B1 (CYP1B1) gene. This gene is a member of the CYP1 gene family and one of the major enzymes involved in the hydroxylation of estrogens, a reaction likely to be relevant in hormonal carcinogenesis. [In dbSNP orientation, the (C) allele encodes the Leu; the (G) the Val.] In a study of 153 Hispanic Caucasians with prostate cancer the rs1056836(G;G) genotype showed decreased risk compared to the more common (C;C) genotype (odds ratio = 0.31, p = 0.04, CI: 0.10-0.96). This report cites another study as indicating that rs1056836(C;C) high-risk stage III and IV breast cancer patients receiving dose-intense paclitaxel in combination with doxorubicin and cyclophosphamide experience a longer progression-free surv...
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rs2046210 is a SNP upstream of the estrogen receptor alpha ESR1 gene. A study of ~7,000 breast cancer cases among Chinese women concluded that rs2046210 was associated with increased risk for the disease; the odds ratio was 1.59 (CI: 1.4-1.82) and 1.36 (CI: 1.24-1.49) for homozygote and heterozygote carriers of a (T) allele (in dbSNP orientation), respectively. A pooled analysis of 31,000+ women found a positive association for rs2046210 and breast cancer risk in Chinese women (odds ratio 1.30, CI: 1.22-1.38, and 1.64, CI: 1.50-1.80, for the CT and TT genotypes (in dbSNP orientation), respectively, p(trend) = 1.54 × 10e-30), Japanese women (1.31, CI: 1.13-1.52, and 1.37, CI: 1.06-1.76, p(trend) = 2.51 × 10e-4), and European-ancestry American women (1.07, CI: 0.99-1.16, and 1.18, ...
Magnitude: 0
Frequency: 55.4%
Repute:Good
References:13
Frequency: 55.4%
Repute:Good
References:13
normal
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
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This SNP in the progesterone receptor PGR gene is not likely to increase the risk of breast cancer.
normal
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rs3803662, a SNP associated with the TNRC9 gene, was one of the four strongest associating SNPs found in a genome-wide association study of over 4,000 breast cancer samples. rs3803662(T;T) have a 1.64-fold greater risk of estrogen receptor-positive tumors In a study of 1,267 breast cancer patients, rs3803662 heterozygote carriers and minor allele homozygote carriers were more likely to be diagnosed before the age of 60 years (p = 0.025) relative to major allele homozygote carriers. breast cancer *rs2981582, rs3803662, and rs889312) showed weak but significant associations with ER-negative disease, the strongest association being for rs3803662 in TNRC9 (1.14 (1.09-1.21)) rs3803662 confirmed in 988 sporadic breast cancer cases and 1,016 controls from the West of Ireland to be associated with...
common in clinvar
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rs1800566 (C609T, Pro187Ser) is a snp within NQO1 (NAD(P)H dehydrogenase (quinone 1)). A Ser (T) at this location denotes the NQO1*2 allele. influences the risk of breast cancer according to the 23andMe blog rs1800566 increases susceptibility to Lung cancer 0.48 times for heterozygotes (CT) [PharmGKB:Curated Risk or phenotype-associated allele: C/T. Phenotype: There was no association between the NQO1*2 polymorphism and the risk of anthracycline-related CHF. Study size: 145. Study population/ethnicity: Nested case-control study was conducted within a cohort of 1979 patients enrolled in the Childhood Cancer Survivor Study who received treatment with anthracyclines and had available DNA. Significance metric(s): OR = 1.04; p = 0.97. Type of association: CO; TOX; ADR.] [OMIM:NAD(P)H DEHYDROGE...
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influences mitosis associated with cancer * breast cancer * colorectal cancer * gastric cancer
common on affy axiom data
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breast cancer *rs10515860 [odds ratio (OR; AA/GG), 0.85; 95% confidence interval (CI), 0.65-1.12; P(trend) = 0.9], *rs299290 [OR (CC/TT), 1.00; 95% CI, 0.87-1.15; P(trend) = 0.7], *rs3756648 (rs7712023) [OR (TT/CC), 0.93; 95% CI, 0.84-1.02; P(trend) = 0.1], *rs299284 [OR (TT/CC), 1.01; 95% CI, 0.76-1.35; P(trend) = 0.5], and *rs13183712 [OR (TT/GG), 1.04; 95% CI, 0.88-1.23; P(trend) = 0.6].
Magnitude: 0
Frequency: 73.2%
Repute:Good
References:1
Frequency: 73.2%
Repute:Good
References:1
common in complete genomics
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cancergenetics The risk of breast cancer was 23% higher in women who had one copy of genetic variant (the A-C-A haplotype: rs7712023-rs299290-rs10515860), and 46% higher in women with two copies. In addition, those women were diagnosed an average of 12 months younger than women from the control group, suggesting that HMMR is linked to early-onset breast cancer. However, a more recent, larger European case-control study found no association between rs10515860 and risk of breast cancer. breast cancer *rs10515860 [odds ratio (OR; AA/GG), 0.85; 95% confidence interval (CI), 0.65-1.12; P(trend) = 0.9], *rs299290 [OR (CC/TT), 1.00; 95% CI, 0.87-1.15; P(trend) = 0.7], *rs3756648 (rs7712023) [OR (TT/CC), 0.93; 95% CI, 0.84-1.02; P(trend) = 0.1], *rs299284 [OR (TT/CC), 1.01; 95% CI, 0.76-1.35; P(tr...
common
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breast cancer rs6503691 rs7211777 Carriers of the AC haplotype, which represents the variant alleles of both SNPs, were at an increased risk (OR = 1.41, 95% CI 1.09-1.82). A decreased risk was observed for carriers of the AT haplotype (OR = 0.60, 95% CI 0.38-0.94). Furthermore, individuals with the AC/GC diplotype were at a significantly increased risk (OR = 1.88, 95% CI 1.13-3.14) A polymorphism associated with STAT3 expression and response of chronic myeloid leukemia to interferon alpha. Association of signal transducer and activator of transcription 3 gene polymorphisms with cervical cancer in Chinese women. Association between polymorphisms in the signal transducer and activator of transcription and dilated cardiomyopathy in the Chinese Han population.
normal
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rs1799969, also known as G241R or +241G/A, is a SNP in the ICAM1 gene. The more common (G) allele encodes the glycine (G). A study of 276 Iranian breast cancer patients concluded (p = 0.008) that rs1799969(A) allele carriers may have a higher risk of developing breast cancer. [PharmGKB:Non-Curated GWAS Results: Novel Association of ABO Histo-Blood Group Antigen with Soluble ICAM-1: Results of a Genome-Wide Association Study of 6,578 Women (Initial Sample Size: 4,570 women; Replication Sample Size: 2,008 women; Risk Allele: rs1799969-G). This variant is associated with Soluble ICAM-1.] [GWAS:None] [GWAS:Soluble ICAM-1]
common in complete genomics
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This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (A).
Magnitude: 0
Frequency: 84.1%
Repute:Good
References:0
Frequency: 84.1%
Repute:Good
References:0
common/normal
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rs10816625 is a SNP in a region of chromosome 9q31.2 that has been associated with breast cancer. In a pooled study of 52 studies totalling 43,160 breast cancer cases in women of European ancestry, plus a further 5795 cases of Asian ancestry, the rs10816625(G) allele was independently associated with increased risk in both Europeans (odds ratio 1.12, CI:1.08-1.17, p = 7.89 × 10e-9) and Asians (odds ratio 1.12, CI:1.06-1.18, p = 2.77 × 10e-5).
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:3
Frequency: 85.0%
Repute:Good
References:3
normal
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rs10754339 is a SNP in the V-set domain containing T cell activation inhibitor 1 VTCN1 gene, which is also known as B7-H4. A study of 500 Chinese Han women with breast cancer (and an equal number of matched controls) concluded that the rs10754339(A;G) genotype and G allele showed a significantly increased risk of breast cancer (odds ratio 1.455, CI: 1.119-1.892, and 1.325, CI: 1.073-1.637, respectively). Additionally, the rs10754339(G;G) genotype was significantly associated with lymph node metastasis and PR status, and the G allele and the (A;G) genotype were respectively associated with lymph node metastasis and ER status.
Magnitude: 0
Frequency: 87.6%
Repute:Good
References:15
Frequency: 87.6%
Repute:Good
References:15
normal
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rs10895068, also known as +331G/A, is a SNP in the progesterone receptor PGR gene. A study of 1,664 postmenopausal breast cancer cases and 2,391 controls led to two conclusions. First, women with at least one rs10895068(A) allele had a 1.3x (CI: 1.04-1.65) increased risk of developing breast cancer. Second, such carriers were at 2.57x (CI: 1.64-4.02) increased risk for breast cancer if they were never postmenopausal hormone users. 2013 meta-analysis suggested association of weak effect with female reproductive (breast, endometrial and ovarian) cancer for A allele (A: OR = 1.063, 95% CI = 1.001-1.129; AA+AG: OR = 1.067, 95% CI = 1.002-1.136). A 2014 meta-analysis that looked only for association with ovarian cancer specifically found no signif...
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associated with breast cancer risk and ovarian cancer More specifically: carriers of two rs2854344(A) alleles have a 25% reduced risk of developing ovarian cancer compared to carriers of two rs2854344(G) alleles, in a survey of ~5,000 women from the US, UK, and Denmark. showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer
normal
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rs4986852 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 1040. The more common rs4986852(G) allele encodes Ser, while the rare rs4986852(A) allele encodes Asn; this variation is also known as Ser1040Asn or S1040N. A well known study published in 1994 looked at 10 family pedigrees with breast cancer and ovarian cancer susceptibility, including 63 breast cancer patients, and discovered what they believed were seven putative disease-causing mutations. rs4986852 was one of these variants. * See also Omim 113705.0011 [OMIM:?]
normal breast cancer risk
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This SNP, a variant in the BRCA1 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. This particular SNP, rs1799950, was actually the only SNP of the 25 to have an increased odds ratio for breast cancer to be over 1.5 in carriers and to also be present at a minor allele frequency of over 5%. The odds ratio calculated was 1.72 (P = 0.0002). The risk (minor) allele is (G). The orientation has been changed to minus manually. We'll see what the bots do to it, with the next major update.
common in complete genomics
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One form of this SNP, known as N991D, A3199G or Asn991Asp for the nonsynonymous change it produces in the BRCA2 protein, has been reported to represent an increased risk for malignant melanoma. In a Polish study of ~600 patients in comparison with ~3700 controls, the rs1799944 SNP was found to have an odds ratio of 1.8. Patients with the homozygous rs1799944(G;G) genotype were present in 0.32% of malignant melanoma cases vs. 0.13% of controls. In two Chinese families with histories of inherited breast cancer, A1093C (Asn289His) in exon 10 and A3199G (Asn991Asp, i.e. rs1799944) in exon 11 of BRCA2 were found occurring together, and they were not seen in pooled control DNA. Risk of non-Hodgkin lymphoma (NHL) in relation to germline variation in DNA repair and related genes. DNA-repair geneti...
common in complete genomics
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This SNP, also known as L1420F, a variant in the ATM gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T). Another large meta-analysis published in 2011, comprising 26,000+ breast cancer cases and almost 30,000 controls from 23 studies in the Breast Cancer Association Consortium, found average odds ratios of 1.05 for heterozygotes and 1.51 for homozygotes of each of 5 ATM gene SNPs, of which this is one. Comprehensive analysis of the ATM, CHEK2 and ERBB2 genes in relation to breast tumour cha...
common in complete genomics
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (G).
common in complete genomics
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T). Association between polymorphisms of the BRCA2 gene and clinical parameters in breast cancer.
common in complete genomics
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T).
normal
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This SNP, also known as F858L, a variant in the ATM gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C). Another large meta-analysis published in 2011, comprising 26,000+ breast cancer cases and almost 30,000 controls from 23 studies in the Breast Cancer Association Consortium, found average odds ratios of 1.05 for heterozygotes and 1.51 for homozygotes of each of 5 ATM gene SNPs, of which this is one. Comprehensive analysis of the ATM, CHEK2 and ERBB2 genes in relation to breast tumour char...
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
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rs726002(C) SNP had an elevated breast cancer risk (odds ratio (OR), 2.09; 95% confidence interval (95% CI), 1.17-3.73)
normal
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rs41293463 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 841. The more common rs41293463(C) allele encodes Arg, while the rare rs41293463(T) allele encodes Trp; this SNP is also known as R841W. A 1996 study of 305 cases in Southern California of breast cancer and ovarian cancer found 3 cases carrying the rs1800709(T) allele. In all three cases, there was a strong family history of breast, ovarian, or other cancers, and family members showed a high concordance of cancer incidence with the presence of this SNP. However, the age of cancer onset was the same as for sporadic cases. The authors conclude that this SNP may explain around 1% (CI: 0-1.7%) of all breast and ovarian cancers, at least for this population. Note: this SNP is rather unlikely to ...
normal
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rs3738414 is a SNP in the V-set domain containing T cell activation inhibitor 1 VTCN1 gene, which is also known as B7-H4. A study of 500 Chinese Han women with breast cancer (and an equal number of matched controls) concluded that the rs3738414(A;A) genotype showed a significantly decreased risk of breast cancer (odds ratio 0.412, CI: 0.203-0.835).
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in complete genomics
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C).
common in complete genomics
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This SNP, a variant in the ATM gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T).
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https://www.23andme.com/health/brca/ i4000377, i4000378, i4000379 are markers that influence your carrier status for breast cancer and ovarian cancer. Note that this SNP is known to have reduced penetrance (~40 - 50%). 185delAG BRCA1 i4000377(D;D) or i4000377(D;I). Alternative names include c.68_69del as well as p.Glu23Valfs∗17 and p.Glu23Valfs. rs80357713 and rs386833395 are the dbSNP rsids for this SNP.
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https://www.23andme.com/health/brca/ i4000377, i4000378, i4000379 are markers that influence your carrier status for breast cancer and ovarian cancer. *5382insC BRCA1 i4000378(I;I) or i4000378(D;I) rs76171189 is the dbSNP rsid for this SNP; it is likely to be included in release b131 of dbSNP.
normal
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https://www.23andme.com/health/brca/ rs80359550 i4000377, i4000378, i4000379 are markers that influence your carrier status for breast cancer and ovarian cancer. *6174delT BRCA2 i4000379(D;D) or i4000379(D;I)
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common/normal
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rs144567652, also known as c.5791C>T, p.Arg1931Ter and R1931X, is a SNP in the FANCM gene. Genotyping 8,635 familial breast cancer cases led to an association with rs144567652, (odds ratio 3.93, CI:1.28-12.11, p=0.017), and two subsequent meta-analyses showed similar [breast cancer associations (odds ratio 3.67, CI:1.04-12.87, p=0.043, and, OR of 3.33, CI:1.09-13.62, p=0.032), respectively. Note: a name used by 23andMe for this SNP is i6050899.
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
common in clinvar
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This SNP, a variant in the CHEK2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C). rs17879961 one of 3 SNPs associated with increased risk of lung cancer [OMIM:?] [GWAS:Lung cancer]
normal
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rs2279744, a variant in the promoter of the MDM2 gene and also known as '-410T-G', 'SNP309', and 'SNP309T>G', has been studied for several years to determine it's role in cancer origin and treatment. The interest primarily stems from the ability of the MDM2 protein to bind to and thereby enhance the degradation of the tumor suppressor protein known as p53. Studies on rs2279744 include: * rs2279744(G) carriers in individuals with cancer tend to develop such cancers on average 12 years earlier than those lacking this allele, and the frequency of rs2279744(G) was greatly increased in those who developed soft tissue sarcomas at a young age. * Individuals with one or more rs2279744(G) alleles who are also carriers of the TP53 rs1042522(C) (arg at aa72) SNP tend to develop cancers earlier tha...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28897672 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 61. The more common rs28897672(T) allele encodes Cys, while the rare rs28897672(G) allele encodes Gly; this variation is also known as Cys61Gly or C61G. A study of 66 Polish families affected with breast cancer or ovarian cancer, often diagnosed at a relatively young age (< 50 years old), screened for BRCA1 mutations by sequencing. The C61G mutation accounted for 20% of the identified mutations in this group of families. * See also Omim 113705.0002 * Also represented as i5010326 by 23andMe [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs28897686, also known as E1250X, c.3748G>T,3867G>T and p.Glu1250Ter, is a variant in the BRCA1 gene. The rare G>T variant allele is considered pathogenic by multiple submitters to ClinVar for breast cancer. Note that a G>A allele also is known, however, the clinical significance is unknown. See also OMIM 113705.0013 Note that the 23andMe representation of this SNP is unclear; on the forward strand (in contrast to dbSNP and SNPedia), the alleles being stated as being tested for rs28897686 and i5010145 are C and T, which would correspond to the G>A allele of unknown clinical significance. The G>T allele that is clinically significant does not appear to be tested on a 23andMe microarray. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28897696, also known as A1708E, c.5123C>A, 5242C>A and p.Ala1708Glu, is a SNP in the BRCA1 gene. The far more common (C) allele encodes the amino acid alanine (A), while the very rare (A) allele encodes glutamic acid (E). An analysis of sequence variants of unknown clinical significance in the BRCA1 and BRCA2 genes concluded that this SNP was among the top 10 (over both genes) likely to lead to breast cancer, with a calculated odds of over 1,000:1 against this just being a spurious association. Although the clinical importance has not been proven, this may still be of use for genetic counseling. More recently, multiple genetic testing labs have reported the rare allele of this SNP to be pathogenic for breast cancer in ClinVar.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs28897756, also known as 9345G>A, c.9117G>A, p.Pro3039= and P3039P is a SNP in the breast cancer 2 BRCA2 gene. The rare rs28897756(A) allele has been linked to increased risk for breast cancer in some Dutch families.. It is considered a causal mutation for breast cancer by UMD and is denoted pathogenic in ClinVar. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. Another name used by 23andMe for this SNP is i5010626.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
complex; generally normal risk
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rs361525 is also known as the TNF-238 SNP, and occasionally the rs361525(A) allele is referred to as 238.2 (with the more common (G) allele being 238.1). This SNP in the tumor necrosis factor-alpha gene has been linked to a wide variety of conditions: * Breast cancer ** A large study of over 5,000 Caucasian women found that rs361525(A) allele carriers were at somewhat elevated risk for breast cancer compared to the (G;G) genotype, with an odds ratio per allele of 1.18, CI: 1.04-1.35, p(trend)= 0.008. ** However, a 2009 European study of 30,000 breast cancer cases, compared to 30,000 controls, found no association, or as they put it, 'persuasive evidence against an overall association between invasive breast cancer risk and (this SNP)'. * Graft versus host disease (GVHD) ** A study of ~100 ...
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs41286296, also known as E755X, c.2263G>T, and p.Glu755Ter, is a variant in the BRCA1 gene. The rare variant allele has been reported in ClinVar as pathogenic for breast cancer by at least three sources.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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rs41293455 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 1443. The more common rs41293455(C) allele encodes Arg, while the rare rs41293455(T) allele encodes a stop codon. Another variant, rs41293455(G), encodes a Gly. A well known study published in 1994 looked at 50 family pedigrees with breast cancer and ovarian cancer susceptibility, discovering what they believed were eight putative disease-causing mutations (four frameshifts, two nonsense mutations) and an additional two missense mutations. rs41293455 was one of these variants. * See also Omim 113705.0016 * See also Omim 113705.0017 [OMIM:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs41293465, also known as R1835X, c.5503C>T, 5622C>T and p.Arg1835Ter, is a variant in the BRCA1 gene. The rare variant allele is considered either pathogenic or likely to be pathogenic for breast cancer by multiple sources in ClinVar.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs41293477, also known as L1053X, c.3158T>G, 3386T>G and p.Leu1053Ter, is a variant in the BRCA2 gene. The rare variant allele is considered pathogenic for breast cancer by three submitters to ClinVar.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs41293497 is a BRCA2 gene variant, with at least two variant alleles: C>G and C>A. [The C>T variant is also possible, however it is a synonymous change that is considered benign.] Alternative names for the pathogenic alleles include Tyr1894Ter, Y1894X, 5910C>G, and 5910C>A. Both the C>G and C>A variants are listed as causal breast cancer mutations in UMD, and as pathogenic by most submitters to ClinVar. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. In addition to presenting rs41293497, 23andMe has an additional C>G SNP at this position known as i5009383 on some of its microarrays.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Normal
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rs45553935 is a tri-allelic SNP in the BRCA1 gene. The reference nucleotide at this position (on the forward strand as listed in dbSNP) is (T); the alternative alleles are (C) and (G). rs45553935(C) corresponds to a BRCA1 change known as Val1736Ala or V1736A, whereas rs45553935(G) corresponds to Val1736Gly or V1736G. This BRCA1 SNP is listed at pathogenic for breast cancer in ClinVar, although the evidence is somewhat indirect. For V1736A, there is now a publication studying the change in depth and concluding it does predispose carriers to breast cancer., The evidence indicating V1736G is pathogenic appears to primarily be computational (i.e. predictive, such as [http://www.ncbi.nlm.nih.gov/pubmed/17305420]) and should be treated with caution. There are breast cancer patients harboring the...
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs55770810, also known as R1699W, is a SNP in the BRCA1 gene. The more common (C) allele encodes the amino acid arginine (R), while the rare (T) allele encodes a tryptophan (W). An analysis of sequence variants of unknown clinical significance in the BRCA1 and BRCA2 genes concluded that this SNP was among the top 10 (over both genes) likely to lead to breast cancer, with a calculated odds of over 1,000:1 against this just being a spurious association. Although the clinical importance has not been proven, this may still be of use for genetic counseling. This SNP is also represented on 23andMe microarrays as i5010082.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs62625306, also known as E797X, c.2389G>T, 2508G>T, and p.Glu797Ter, is a SNP in the BRCA1 gene. The rare variant allele is considered pathogenic for breast cancer by multiple sources in ClinVar. See also OMIM 113705.0023
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs62625307, also known as Q1200X, c.3598C>T, and p.Gln1200Ter, is a SNP in the BRCA1 gene. The rare variant allele is considered pathogenic for breast cancer according to multiple sources in ClinVar.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs80359205, also known as W3106X, c.9317G>A and p.Trp3106Ter, is a variant in the BRCA2 gene considered pathogenic for breast cancer in ClinVar.
common in complete genomics common for Caucasians on the 23andme platform
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also known as rs28933380 related to colorectal cancer, FAMILIAL, Ashkenazi The APC I1307K mutation is primarily found in people of Ashkenazi Jewish heritage (Jews of Eastern European or Russian ancestry). Researchers believe that 6% of Ashkenazi Jews carry this gene mutation, making them at a significantly higher risk for developing colorectal cancer. It is also found among Sephardi and Mizrahi Jews and Muslim and Christian Palestinian Arabs, as well as Negev Bedouin. Many patients with colorectal cancer experience no symptoms in the early stages. In fact, symptoms may not appear until the disease is in advanced stage. Routine colorectal screening is very important. Even children from 11 years of age should be screened if there is a family history of colorectal cancer. * APC I1307K and Col...
normal
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(C;C) predisposes to papillary thyroid carcinoma. Among 42 patients with familial breast cancer and 82 patients with ovarian cancer, those with at least one rs2910164(C) SNP tended to have been diagnosed at an earlier age than those with only (G) alleles. For the breast cancer patients, the difference in median age was between 45 vs 56 (p = 0.029) and for ovarian cancer patients, 45 vs 50, (p = 0.014). (G;G) males were two-fold more susceptible to hepatocellular carcinoma (OR = 2.016, 95% CI = 1.056-3.848, P = 0.034) perhaps an ambiguous flip? [OMIM:MICRO RNA 146A; MIRN146A]
but the rare allele is protective
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rs1045485, also known as D302H, is a SNP in the caspase-8 CASP8 gene. Several large studies indicate that the (C) allele of this SNP, located in exon 10 of the CASP8 gene, may reduce the risk of breast cancer in a dose dependent manner. The odds ratio is 0.89 for (C;G) and 0.74 for (C;C) carriers. article cancergenetics A 4-SNP haplotype including rs1045485 was significantly associated with breast cancer in a large European study (3,000+ cases, 3,000+ controls), with a per allele odds ratio of 1.3 (CI:1.12-1.49). chronic lymphocytic leukemia rs2266690 rs17028658 rs4505265 rs1045485 rs2779251 rs3136687 showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer No association seen between ...
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Chinese breast cancer rs11225297(T) improved survival. (A;T) (OS HR: 0.7, 95% CI: 0.5-0.9) and (T;T) (OS HR: 0.3, 95% CI: 0.1-0.8)
common in complete genomics
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T). [GWAS:Breast cancer]
common in complete genomics
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This SNP, a variant in the ATM gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T).
common in complete genomics
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This SNP, a variant in the ATM gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C).
common on affy axiom data
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rs1800054, also known as S49C, is a SNP in the ATM gene. A large meta-analysis published in 2011, comprising 26,000+ breast cancer cases and almost 30,000 controls from 23 studies in the Breast Cancer Association Consortium, found average odds ratios of 1.05 for heterozygotes and 1.51 for homozygotes of each of 5 ATM gene SNPs, of which this is one. A common coding variant in CASP8 is associated with breast cancer risk. Two-stage case-control study of common ATM gene variants in relation to breast cancer risk. Single-nucleotide polymorphisms in the p53 signaling pathway. Gene-environment interactions in 7610 women with breast cancer: prospective evidence from the Million Women Study. [OMIM:?]
common in complete genomics
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rs28997576, aka Cys557Ser or C557S, is a missense variant in the BRCA1 associated RING domain 1 BARD1 gene on chromosome 2. Researchers suggest that BARD1 Cys557Ser (rs28997576) is an ancient variant that confers risk of single and multiple primary breast cancers, and this risk is amplified in carriers of the BRCA2 999del5 (codon 257, exon 9) mutation. For just the rs28997576(C;G) individuals, the reported odds ratio was 1.82 (CI: 1.11-3.01, p = 0.014), but if the person also carries a rs80359671 or rs80359675 BRCA2 999del5 variant, the odds ratio was reported as 3.11 (CI: 1.16-8.40, p = 0.046). Family history was associated with (slightly) increased risk. In 300 breast cancer cases in South Americans, rs28997576(C;G) was associated with increased breast cancer risk if, and only if, there ...
common in clinvar
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rs41293461, also known as W1718X, c.5153G>A and p.Trp1718Ter, is a variant in the BRCA1 gene considered pathogenic for breast cancer in ClinVar.
208 snps
(hide) Canavan disease
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs12948217, also known as Y231X or Tyr231Ter, is a SNP in the ASPA gene. According to 23andMe, only the A allele at rs12948217 confers risk to Canavan disease. A person with the CC, CT, or TT alleles is not a carrier; someone with the AC or AT alleles is a carrier; and people with two AA alleles are affected with the disease. [OMIM:[[Canavan disease]]]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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rs28940279, also known as E285A or Glu285Ala, is a SNP in the ASPA gene. rs28940279 is one of several known causal SNPs of Canavan disease. Canavan disease is a degenerative disease of the nervous system. It is a childhood onset disease which begins in early infancy. It is characterized by disordered muscular behavior (e.g., hypotonia, hyperextension) and neurological symptoms, such as blindness, developmental and cognitive delays. The neurological findings appear to be due to demyelination and leukodystrophy. Histology indicates the presence of spongy degeneration; cytology confirms astrocytic swelling of normal neurons and abnormality of astrocyte mitochondria. Ultimately, sufferers become extremely ill and die on average at 18 months of age. rs28940279 is a SNP in the aspartoacylase ASP...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs28940574, also known as A305E or Ala305Glu, is a SNP in the ASPA gene. rs28940574 is one of several known causal SNPs of Canavan disease. [OMIM:[[Canavan disease]]]
3 snps
(hide) Cancer
1.6x increased risk for prostate cancer; also other cancers 1.4 times as likely to develop colorectal cancer
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. This SNP has also been reported to influence the cancer-risk-decreasing effect of aspirin. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neig...
Mean Survival Time of 17 months for esophageal squamous-cell carcinoma
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rs1050631 is a SNP on chromosome 18q12 in exon 6 of SLC39A6 gene, associated with length of survival in esophageal squamous-cell carcinoma(ESCC). The SNP is located in the 5’ UTR of SLC39A6. In a study, a genome-wide scan of SNPs to identify variants associated with length of survival in 1331 individuals with ESCC was performed, and was validated by two independent sets, including 1962 individuals with ESCC (1308 and 654 individuals in two different replications). The hazard ratio for death (odds ratio) (T; T) and (C; T) from ESCC in the 1331 test cases was 1.34 (95% confidence interval (CI) = 1.17−1.53; P = 7.78 E-6). For the combined data, hazard ratio of death similarly was found to be 1.34 (95% CI = 1.17−1.53; P = 7.78 E−6). The combined discovery and replicatio...
NAT2 slow metabolizer
Most non-Scandinavian Caucasians and approximately half of African-Americans are slow metabolizers. This variation is important because of its primary role in the deactivation of many chemicals in the body's environment, including those produced by caffeine and cigarettes as well as aromatic amine and hydrazine drugs used medicinally. In general, slow metabolizers have higher rates of certain types of cancer and are more susceptible to side effects from chemicals metabolized by NAT2. According to this source 6 snps determine NAT2 metabolism. The way their genotypes interact is very complex, which makes this one of the largest genosets in SNPedia. The SNPs are: *rs1208 *rs1041983 *rs1799929 *rs1799930 *rs1799931 *rs1801280
NAT2 Slow metabolizer
Most non-Scandinavian Caucasians and approximately half of African-Americans are slow metabolizers. This variation is important because of its primary role in the deactivation of many chemicals in the body's environment, including those produced by caffeine and cigarettes as well as aromatic amine and hydrazine drugs used medicinally. In general, slow metabolizers have higher rates of certain types of cancer and are more susceptible to side effects from chemicals metabolized by NAT2. This prediction and that of gs156 of NAT2 metabolizer phenotype is based on using 2 SNPs, rs1041983 and rs1801280. An alternative prediction of NAT2 metabolizer status based on using more SNPs (6) is used by genosets gs138, gs139, and gs140.
~0.80x reduced cancer risk
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rs763110, also known as -844C>T, is a SNP in the FAS ligand FASLG gene. A meta-analysis of 19 published studies, including 11,105 cancer cases and 11,372 controls, concluded that the rs763110(C;T) and (T;T) genotypes were associated with a significantly reduced (about 0.80x) cancer risk of all cancer types.
1.5x increased bladder cancer risk
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rs9642880 is a SNP located in chromosome region 8q24, a region that has been linked to prostate, breast, and colon cancer. A study ultimately totaling over 4,000 bladder cancer patients of European ancestry (and 40,000 controls) concluded that individuals carrying two copies of rs9642880(T) were at 1.49x increased risk (allele-specific odds ratio = 1.22, p = 9 x 10e-12) for the disease. This SNP was not associated, however, with risk for prostate, breast, or colon cancer. Another study in Chinese populations found similar results in regard to bladder cancer. rs9642880(T;T) estimated risk of developing 1.49 times that of noncarriers. 1,803 urinary bladder cancer cases and 34,336 controls. No association with prostate, colorectal and breast cancers. In contrast to GSTM1 SNPs, the rs9642880(T...
Magnitude: 2
Frequency: 22.1%
Repute:Good
References:61
Frequency: 22.1%
Repute:Good
References:61
decreased risk for colorectal cancer and lung cancer source
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miRNA sequences and non-small cell lung cancer rs11614913 SNP in hsa-mir-196a2 was associated with survival in individuals with NSCLC. Specifically, survival was significantly decreased in individuals who were homozygous CC at SNP rs11614913. microRNA 1,009 breast cancer cases and 1,093 controls in a population of Chinese women *rs11614913 in hsa-mir-196a2 T>C 1.23; 95% confidence interval [CI], 1.02-1.48 *rs3746444 in hsa-mir-499 A>G OR 1.25; 95% CI, 1.02-1.51 Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Signatures of purifying and local positive selection in human miRNAs. MicroRNA polymorphisms: the future of pharmacogenomics...
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
2x higher risk for skin cancer; possibly other cancers
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rs25487 is a SNP also known as Gln399Arg, located in the DNA repair gene XRCC1. The (A) allele encodes the Gln amino acid. In one study of ~1000 Caucasians, the rs25487(A;A) genotype had significantly reduced risk of both basal cell [BCC; odds ratio 0.7, CI: 0.4-1.0] and squamous cell cancer (SCC; odds ratio 0.6, CI: 0.3-0.9). In a study of ~300 Koreans, rs25487(A;G) and (G;G) genotypes had an approximately 2-fold increased risk of basal cell cancer compared to rs25487(A;A) individuals (adjusted odds ratio 2.324, CI: 1.11-4.86, respectively). A small study (113 cases) of Hispanics with non-small cell lung cancer found an odds ratio of 1.52 per rs25487(A) allele (CI: 1.01-2.28). A study of 200 patients with Hodgkin disease compared to controls concluded that some risk was associated with th...
Normal (lower) risk of Type 2 Diabetes and Gestational Diabetes. Normal insulin secretion in the pancreas. This has been confirmed in most races.
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This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). This SNP is also known as IVS3C>T. rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. Full text of the paper is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse population Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion...
Alcohol Flush: Normal, doesn't flush. Normal hangovers. Normal risk of Alcoholism. Normal risk of Esophageal Cancer. Disulfiram is effective for alcoholism. Two working copies of Aldehyde Dehydrogenase (ALDH2) mean you won't turn bright red when you drink alcohol, unlike most Asians. After your body turns alcohol into the dangerous acetaldehyde, this gene quickly turns the acetaldehyde into vinegar. It also stops the acetaldehyde in cigarettes from causing Esophageal Cancer. It reduces hangovers compared to Asians, but less hangovers and flushing obviously increases the risk of alcoholism. Alcoholism can be treated effectively with the drug Disulfiram (Antabuse) which would stop this gene from working and cause the Asian flush in non-Asians. PMC2659709 [http://www.ncbi.nlm.nih.gov/pmc/art...
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rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Disulfiram (...
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
~1.2x increased risk for several types of cancer
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rs401681 is a SNP in the CLPTM1-like CLPTM1 gene. The following studies span several types of cancer, and over 30,000 cases and 45,000 controls. deCODE press release reports rs401681 linked to basal cell carcinoma and many cancers for individuals with shorter telomeres, whereas those with long telomeres are at greater risk of melanoma. Neighboring rs2736098 also increases risk of cancer by affecting telomerase reverse transcriptase. The risk of these different cancers conferred by these two SNPs appears to be independent. 23andMe blog rs2736098 and rs401681 linked to many cancers, including susceptibility to pancreatic cancer However, a very large study (encompassing thousands of cases and controls) found no association between rs401681 and either (1) mean telomere length, or, (2) breast c...
Lower C-Reactive Protein levels. 1.2x increased risk overall for cancers. This causes a lower median hsCRP Level of 1.40 mg/L in women. Strangely this was associated with a higher overall cancer risk (in Finnish people).
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rs1892534 is a SNP that was originally associated with C-reactive protein levels, and given other findings that suggest C-reactive protein levels may be predictive of cancer risk, was thought to be linked to cancer risk. A large study pooling data from 3 Finnish studies totaling over 18,000 individuals concluded that while the rs1892534(A) allele was not likely to be causative (relative to cancer), it is associated with increased risk for cancer overall. The odds ratio for 1 or 2 such alleles was 1.05 (CI: 0.90 - 1.23) and 1.2 (CI: 1.01 - 1.42) overall. Two other CRP SNPs (rs1169300 and rs2464196) were specifically associated with increased lung cancer risk. CRP SNPs were not associated with colorectal, prostate or breast cancer risk. [PharmGKB:Curated GWAS Results: Loci Related to Metabo...
normal oral/throat cancer risk; more frequent alcohol consumption
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A SNP in rs1229984 encodes a form of the alcohol dehydrogenase ADH1B gene that significantly reduces the clearance rate of alcohol from the liver. This SNP is also known as Arg48His, with the (G) allele corresponding to the Arg and the (A) to the His. Known in the literature as ADH2*2 or sometimes ADH1B*2, the allele with increased activity (meaning more rapid oxidation of ethanol to acetaldehyde) is His48, encoded by rs1229984(A). Individuals with one or especially two ADH2*2 alleles, ie genotypes rs1229984(A;G) or rs1229984(A;A) are more likely to find drinking unpleasant and have a somewhat reduced risk for alcoholism. A study of over 3,800 cases of 'upper aerodigestive' cancers (mouth/throat, voice box, and esophageal cancers) concluded that the rs1229984(A) allele (in dbSNP orientatio...
0.68x decreased risk of oral/throat cancers
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rs1573496 is a SNP in the ADH7 alcohol dehydrogenase 7 gene. A study of over 3,800 cases of 'upper aerodigestive' cancers (mouth/throat, voice box, and esophageal cancers) concluded that the rs1573496(G) allele has a protective effect. Carriers of this allele had a 0.68x (decreased; p=10<sup>-9</sup>) risk of having one of these cancer types. A Genome-Wide Association Study of Upper Aerodigestive Tract Cancers Conducted within the INHANCE Consortium. The data in this paper, makes it seem that (G;G) was much more common. This is inconsistent with the HapMap frequencies, suggesting the sequence may have been flipped. Diplotype trend regression analysis of the ADH gene cluster and the ALDH2 gene: multiple significant associations with alcohol dependence. Multiple ADH genes modulat...
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rs2228001, also known as Lys939Gln, K939Q, and K940Q, is a SNP in the DNA nuclear excision repair gene xeroderma pigmentosum complementation group C XPC gene. The Lys (K) allele is encoded by the rs2228001(A) allele. A meta-analysis of 16 studies with 6797 cancer cases and 9018 controls concluded that rs2228001(C;C) homozygotes had an increased overall cancer risk (odds ratio of 1.16, CI: 1.05-1.28) compared with (A;A) homozygotes. This was primarily a risk for lung cancer. [PharmGKB:Curated Risk or phenotype-associated allele: Not specified. Phenotype: This SNP was associated with clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): p = 0.0045 (ANOVA); p = 0.052 (QMIS); p = 0.0004 (KW) Type of association...
normal
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827 males and 709 females, 606 subjects without cancer and 930 subjects with various cancers *rs1041981(A;C) (C804A, T60N) associated with lung cancer (CA + AA: CC, adjusted OR = 0.60, 95% CI = 0.37 - 0.97), in males but not in females [OMIM:MYOCARDIAL INFARCTION, SUSCEPTIBILITY TO]
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Associated with at least one 'mortality outcome' in a study of ~10,000 individuals. 827 males and 709 females, 606 subjects without cancer and 930 subjects with various cancers *rs2229094(A;A) (T495C, C13R) associated with gastric cancer (TC + CC: TT, adjusted OR = 1.68, 95% CI = 1.06 - 2.65) in males but not in females
normal
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rs2228000, also known as Ala499Val and A499V, is a SNP in the DNA nuclear excision repair gene xeroderma pigmentosum complementation group C XPC gene. The Val (V) allele is encoded by the rs2228000(T) allele. A meta-analysis of 11 studies with 5581 cancer cases and 6351 controls concluded that rs2228000(T;T) homozygotes had an increased overall cancer risk (odds ratio of 1.24, CI: 1.08-1.42) compared with (C;C) homozygotes. This was primarily a risk for bladder cancer.
normal asthma risk in certain populations
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common...
normal
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rs1801394, also known as A66G or Ile22Met, is a SNP in the methionine synthase MTRR gene. This gene encodes one of the two enzymes involved in the production of methionine (the other is MTR). The protein encoded by an rs1801394 allele has a lower affinity for MTR () and is inconsistently associated with homocysteine level, although it is a risk factor for neural tube defects () and Down syndrome () in conditions of higher homocysteine. Based on a study of British patients with primary brain tumors, (1,005 glioma cases and 631 meningioma cases), rs1801394(G;G) individuals were at higher risk for meningioma (odds ratio 1.41, CI: 1.02-1.94). In general, genotypes associated with increased 5,10-methylenetetrahydrofolate levels are associated with elevated risk for these types of brain cancer. ...
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rs1801131 is a SNP in the MTHFR gene, representing an A>C mutation at mRNA position 1298, resulting in a glu429-to-ala (E429A) substitution (hence this SNP is also known as A1298C or E429A). A diplotype (according to the authors, but perhaps actually a genoset) of rs1801131 and rs1801133 has been linked to increased risk for several types of brain cancer. The highest risk of meningioma was associated with heterozygosity for both MTHFR SNPs (odds ratio 2.11, CI: 1.42-3.12, p=0.002). The corresponding odds ratio for glioma was 1.23 (CI: 0.91-1.66, p=0.02. In general, risks were increased with genotypes associated with reduced MTHFR activity. rs1801131 shows no consistent association with schizophrenia overall in 12 studies totaling 3,000+ patients [PharmGKB:Curated Risk or phenotype-asso...
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
normal
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rs2464196 is a SNP that was originally associated with C-reactive protein levels, and given other findings that suggest C-reactive protein levels may be predictive of cancer risk, was thought to be linked to cancer risk. A large study pooling data from 3 Finnish studies totaling over 18,000 individuals concluded that while this SNP is not likely to be causative (relative to cancer), it and one other CRP SNP (rs1169300) are associated with increased risk for lung cancer. The odds ratio for minor alleles of either SNP was about 1.5x and 2x for heterozygotes and homozygotes, respectively. One other CRP SNP (rs1892534) was associated with increased overall cancer risk. CRP SNPs were not associated with colorectal, prostate or breast cancer risk. [PharmGKB:Curated In a candidate gene-based ass...
normal
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rs1169300 is a SNP that was originally associated with C-reactive protein levels, and given other findings that suggest C-reactive protein levels may be predictive of cancer risk, was thought to be linked to cancer risk. A large study pooling data from 3 Finnish studies totaling over 18,000 individuals concluded that while this SNP is not likely to be causative (relative to cancer), it and one other CRP SNP (rs2464196) are associated with increased risk for lung cancer. The odds ratio for minor alleles of either SNP was about 1.5x and 2x for heterozygotes and homozygotes, respectively. One other CRP SNP (rs1892534) was associated with increased overall cancer risk. CRP SNPs were not associated with colorectal, prostate or breast cancer risk.
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influences mitosis associated with cancer * breast cancer * colorectal cancer * gastric cancer
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y or Cys282Tyr mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who act...
normal
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rs2279744, a variant in the promoter of the MDM2 gene and also known as '-410T-G', 'SNP309', and 'SNP309T>G', has been studied for several years to determine it's role in cancer origin and treatment. The interest primarily stems from the ability of the MDM2 protein to bind to and thereby enhance the degradation of the tumor suppressor protein known as p53. Studies on rs2279744 include: * rs2279744(G) carriers in individuals with cancer tend to develop such cancers on average 12 years earlier than those lacking this allele, and the frequency of rs2279744(G) was greatly increased in those who developed soft tissue sarcomas at a young age. * Individuals with one or more rs2279744(G) alleles who are also carriers of the TP53 rs1042522(C) (arg at aa72) SNP tend to develop cancers earlier tha...
2 genosets 27 snps
(hide) Cancer progression and tumor cell motility
normal
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rs351855, a SNP in the fibroblast growth factor receptor 4 (FGFR4) gene, is also known as the Gly388Arg variant. The rs351855(T) allele encodes the risk (Arg) allele. The Arg form of this SNP is likely to cause a harder to treat version of node-positive breast cancer, including reducing the efficacy of Herceptin, based on a study of 372 patients. A study of ~500 Japanese prostate cancer patients found that individuals with a rs351855(T;T) genotype had a 2.2- and 1.9-fold increased risk of prostate cancer and benign prostate hyperplasia (BPH), and a 1.8-fold increased risk of metastatic prostate cancer compared to the (C;C) genotype. A meta-analysis published in 2011, surveying a total of 2,618 cases of prostate cancer, concluded that the odds ratio per rs351855(T) allele was 1.17 (CI: 1.07...
1 snp
(hide) Celiac disease
increased risk for celiac disease increased resistance to bacterial infections
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rs3184504 is a nonsynonymous SNP in the SH2B3 gene, and it is also known as R262W. In a recent (2008) study of non-HLA SNP associations of 1600+ celiac disease patients, this SNP was considered one of the most significant. The odds ratio for the minor allele was 1.19 (CI:1.10-1.30, p=1.33x10e-7). rs653178, another SNP in strong linkage disequilibrium (r<sup>2</sup>>0.99) with rs3184504, was also associated with celiac disease. associated with type-1 diabetes 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 23andMe blog blood pressure Pharmacogenetic implications for eight common blood pressure-associated...
Frequency: 14.2%
References:1
References:1
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[GWAS:Celiac disease]
Frequency: 15.9%
References:8
References:8
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[GWAS:Ulcerative colitis]
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[GWAS:Celiac disease]
Frequency: 19.5%
References:1
References:1
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[GWAS:Celiac disease]
Frequency: 23.0%
References:1
References:1
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[GWAS:Celiac disease]
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Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23. Replication of recently identified associated single-nucleotide polymorphisms from six autoimmune diseases in Genetic Analysis Workshop 16 rheumatoid arthritis data. Survival dimensionality reduction (SDR): development and clinical application of an innovative approach to detect epistasis in presence of right-censored data. Risk alleles for systemic lupus erythematosus in a large case-control collection and associations with clinical subphenotypes. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. [GWAS:C...
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Celiac Disease [GWAS:Vitiligo]
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[GWAS:Celiac disease]
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Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. [PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs2816316-C).] [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 7; CELIAC7] [GWAS:Celiac disease] [GWAS:Celiac disease]
Frequency: 30.1%
References:2
References:2
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23andMe blog risk factors contributing to both celiac disease and Crohn’s disease in nearly 10,000 subjects with either disease and more than 10,000 healthy individuals, all of European ancestry. The CC genotypes at both rs10188217 and rs212388 were associated with slightly higher odds of either disease compared to the CT genotype, and the TT genotypes at both SNPs were associated with slightly lower odds. [GWAS:None]
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[GWAS:Celiac disease]
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Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. Fine mapping the TAGAP risk locus in rheumatoid arthritis. [PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs1738074-A).] [OMIM:CEL...
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rs2395182 is one of three HLA region SNPs used to tag the DQ2.2 haplotype in gs221.
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[GWAS:Celiac disease]
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[GWAS:Celiac disease]
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[GWAS:Celiac disease]
Frequency: 39.8%
References:14
References:14
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[GWAS:Celiac disease]
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Genome-wide interaction-based association analysis identified multiple new susceptibility Loci for common diseases. [GWAS:Celiac disease]
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[GWAS:Celiac disease]
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The G allele is associated with 1.3 times higher odds of primary biliary cirrhosis. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. Primary Biliary Cirrhosis: Preliminary Research [GWAS:Celiac disease]
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rs2305764 is a SNP in the untranslated region of the MYO9B gene that has been associated with celiac disease, and thus gluten intolerance. The risk allele is rs2305764(T) as named in accordance with dbSNP. [OMIM:MYOSIN IXB; MYO9B]
Frequency: 44.6%
References:2
References:2
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[GWAS:Celiac disease]
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Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Shared and distinct genetic variants in type 1 diabetes and celiac disease. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 9; CELIAC9] [GWAS:Celiac disease]
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[GWAS:Celiac disease]
Frequency: 50.0%
References:1
References:1
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[GWAS:Celiac disease]
Frequency: 50.4%
References:1
References:1
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[GWAS:Celiac disease]
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Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. Investigation of type 1 diabetes and coeliac disease susceptibility loci for association with juvenile idiopathic arthritis. [PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs1464510-A).] [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 11; CELIAC11] [GWAS:Celiac disease] [GWAS:Celiac disease]
Frequency: 52.2%
References:1
References:1
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[GWAS:Celiac disease]
Frequency: 53.1%
References:1
References:1
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[GWAS:Celiac disease]
Frequency: 56.6%
References:1
References:1
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[GWAS:Celiac disease]
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[GWAS:Celiac disease]
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[GWAS:Celiac disease]
Frequency: 61.9%
References:2
References:2
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[GWAS:Celiac disease]
Frequency: 62.8%
References:8
References:8
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[PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs13015714-C).] [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 8; CELIAC8] [GWAS:Atopic dermatitis] [GWAS:Celiac disease]
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[GWAS:Celiac disease]
1.1x increased risk for schizophrenia
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rs6932590 is a SNP that is postulated to have a role in conferring increased susceptibility for schizophrenia. rs6932590 lies in the major histocompatibility complex (MHC) region on chromosome 6, a region that codes for several genes with significant roles in autoimmunity, such as human leukocyte antigens. Specifically, rs6932590 lies in an intergenic region between PRSS16 (a serine protease expressed in the thymus that plays a role in positive T cell selection) and POM121L2 (a membrane glycoprotein) . The T allele at rs6932590 purportedly confers an increased risk for schizophrenia, with reported odds ratios of 1.16 and 1.31 . === Evidence === One large-scale case-controlled genome-wide association study (GWAS) that examined differential genotypes in individuals with schizophrenia, found ...
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A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Polymorphisms in the CD28/CTLA4/ICOS genes: role in malignant melanoma susceptibility and prognosis? Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. [GWAS:Celiac disease]
Frequency: 68.8%
References:1
References:1
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[GWAS:Celiac disease]
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[GWAS:Celiac disease]
Frequency: 71.4%
References:2
References:2
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[GWAS:Celiac disease]
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[GWAS:Celiac disease]
Frequency: 78.8%
References:14
References:14
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Of SNPs outside the HLA region, this SNP and one other (rs6822844) in the region of the IL21 gene showed the strongest association with celiac disease in a study of ~800 Caucasian patients and a meta-analysis of two further populations. [OMIM:KIAA1109 GENE; KIAA1109] [GWAS:Rheumatoid arthritis]
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linked to Crohn's disease and type-1 diabetes Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants. Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1). The expanding genetic overlap between multiple sclerosis and type I diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1. Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cyto...
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[GWAS:Celiac disease]
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[GWAS:Celiac disease]
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This SNP, rs653178, is basically a proxy (r<sup>2</sup>>0.99) for rs3184504, as both are associated with celiac disease; see rs3184504 for more details. This SNP is also associated with risk of hypertension. 23andMe blog blood pressure [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 13; CELIAC13] [GWAS:Celiac disease]
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Newly identified genetic risk variants for celiac disease related to the immune response. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. Shared and distinct genetic variants in type 1 diabetes and celiac disease. Association study of the IL18RAP locus in three European populations with coeliac disease. Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associatio...
Magnitude: 0
Frequency: 64.6%
Repute:Good
References:17
Frequency: 64.6%
Repute:Good
References:17
Magnitude: 0
Frequency: 67.3%
Repute:Good
References:1
Frequency: 67.3%
Repute:Good
References:1
common on affy axiom data
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Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. [GWAS:Celiac disease]
common in complete genomics
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People with the human leukocyte antigen (HLA) genotype DRB1*0301-DQA1*0501-DQB1*0201/DRB1*04-DQA1*0301-DQB1*0302 (more simply known as 'DR3/4-DQ8') are at the highest risk of developing type-1 diabetes. The rs2040410(A) allele is associated with DRB1*0301, and the rs7454108(C) allele is associated with DQB1*0302 (and thus DQ8). Instead of more traditional antibody-based tests, two SNPs (rs2040410 and rs7454108) can be used to identify the presence or absence of the DR3/4-DQ8 genotype and thus the highest-risk heterozygous genotype associated with type-1 diabetes. For users of Promethease, this is determined via Gs121.
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[GWAS:Celiac disease]
common on affy axiom data
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association with rheumatoid arthritis and type-1 diabetes point to a general risk locus for autoimmune diseases. Also, of SNPs outside the HLA region, this SNP and one other (rs13119723) in the region of the IL21 gene showed the strongest association with celiac disease in a study of ~800 Caucasian patients and a meta-analysis of two further populations. A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci. Association study of IL2/IL21 and FcgRIIa: significant association with the IL2/IL21 region in Scandinavian coeliac disease families. Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Gene variants influencing mea...
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
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rs7775228 is one of three HLA region SNPs used to tag the DQ2.2 haplotype in gs221. rs7775228(T) was found to be associated with increased risk for osteoarthritis among Japanese, but not Europeans, with an odds ratio of 1.34 (CI: 1.21-1.49, combined p = 2.43×10e?8). This SNP is also in linkage disequilibrium with rs10947262, which was found to be associated in multiple populations with osteoarthritis. 23andMe reports that the C allele at rs7775228 is associated with hay fever (allergic rhinitis and allergy to grass pollen. Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants. [GWAS:None]
Magnitude: 0
Frequency: 81.5%
Repute:Good
References:14
Frequency: 81.5%
Repute:Good
References:14
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs17810546-G).] [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 10; CELIAC10] [GWAS:Celiac disease] [GWAS:Celiac disease]
average
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In at least UK populations, and perhaps others, SNP rs2187668 is a tag SNP for the HLA-DRB1*0301 allele. The HLA-DRB1*0301 allele is the allele presenting the highest risk for developing lupus, and it appears to act in a dominant manner (i.e. inheriting 2 copies is no worse than inheriting 1 copy). In dbSNP orientation, the risk allele is rs2187668(A), with an odds ratio of 2.3x (CI: 1.7 - 3.2, permuted p < 0.0001). From individuals with the most common rs2187668(G;G) genotype, risk is reduced for celiac disease, with an odds ratio of 0.30x according to a study of ~800 patients. rs2187668(A) also tags the tightly linked DQB1*0201 allele, which in turn is linked to DQA1*0501; together, these are known as the DQ2.5 haplotype. This is the most common haplotype associated with celiac diseas...
Magnitude: 0
Frequency: 85.7%
Repute:Good
References:1
Frequency: 85.7%
Repute:Good
References:1
62 snps
(hide) Central core disease
Magnitude: 0
Repute:Good
References:11
Repute:Good
References:11
common in clinvar
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rs28933396, aka p.Arg2435His or p.R2435H, is a SNP in the RYR1 gene associated with central core disease. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: Different RYR1 variants are associated with significant differences in in vitro contracture tests (IVCT) and creatine kinase (CK) phenotypes; more specifically, the variants p.R163C, p.R2163H (rs28933999 G to A), p.R2435H (rs28933396 G to A), and p.T4826I were significantly associated with a more severe form of each quantitative phenotype Study size: 450. Study population/ethnicity: Malignant hyperthermia -susceptible individuals (Cau...
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
common in clinvar
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rs63749869, aka p.Arg4861His or p.R4861H, is a SNP in the RYR1 gene associated with central core disease as well as a congenital neuromuscular disease. [OMIM:?]
2 snps
(hide) Cervical cancer
1.43x increased risk of developing psoriasis and psoriatic arthritis
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IL12B gene SNP, part of a haplotype with rs6887695 associated with psoriasis. A study of 500+ patients with psoriatic arthritis (PsA) concluded that the odds ratio for rs3212227(A;A) carriers was 1.43 (CI: 1.17-1.76). The effect sizes observed in patients with PsA appear to be smaller than those previously reported in patients with psoriasis, suggesting that both loci are primarily associated with psoriasis susceptibility rather than primarily with psoriatic arthritis. rs568408 GA/AA and rs3212227 AC/CC variant genotypes were associated with a significantly increased risk of cervical cancer [adjusted odds ratio, 1.43; 95% confidence interval (CI), 1.06-1.93; and adjusted odds ratio, 1.30; 95% CI, 0.97-1.75, respectively]. subjects carrying variant genotypes of both loci had a 1.82-fold (95...
Frequency: 0.9%
References:1
References:1
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[GWAS:Cervical cancer]
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rs1799929 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799929(T). When this SNP is indicative of carrying a NAT2*5A allele, the following may be relevant: A study (based on only 42 patients) found that women with the NAT2*5A slow genotype (which presumably means rs1799929(T;T)) had a significantly higher risk of cervical cancer compared with individuals with the NAT2*5A fast genotype (i.e. carriers of only one rs1799929(T) allele), with a reported odds ratio of 7.469 (CI: 1.6-33.3, p=0.008). [PharmGKB:Curated in vitro study; PK: 20-fold reduction...
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[GWAS:Cervical cancer]
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[GWAS:Cervical cancer]
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rs1946518 and rs1946519 may influence cervical cancer
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[GWAS:Cervical cancer]
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[GWAS:Cervical cancer]
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rs8067378 is the strongest associating SNP from a region of chromosome 17q21 found in a large (ultimately over 7,000 patients in 3 populations) genome-wide association study of childhood asthma. Since the associated SNPs were also strongly associated (p < 10<sup>-22</sup>) in cis with transcript levels of from the ORMDL3 gene, the authors concluded that genetic variants regulating ORMDL3 expression are determinants of susceptibility to childhood asthma. Assessing the reproducibility of asthma candidate gene associations, using genome-wide data. Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene. Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in mexican children. Allele-specific chromatin remode...
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cervical cancer susceptibility *rs9296925, P = 0.0193; *rs853360, P = 0.0035; *rs9230, P = 0.0011; *rs9370729, P = 0.0012; *rs750749, P = 0.0133
10 snps
(hide) Charcot-Marie-Tooth
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
4 snps
(hide) Charcot-Marie-Tooth disease
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Mutations in a gene encoding a novel SH3/TPR domain protein cause autosomal recessive Charcot-Marie-Tooth type 4C neuropathy. [OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
9 snps
(hide) Cholesterol
CYP3A5 non-expressor
This is common for Caucasians, but rare for African populations. As a CYP3A5 non-expressor you are unable to metabolize some common medications. This influences the synthesis of cholesterol, steroids and other lipids. The enzyme metabolizes drugs such as olanzapine, tacrolimus, nifedipine and cyclosporine as well as the steroid hormones testosterone, progesterone and androstenedione.
lower risk of ischemic stroke
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rs2943634 is a SNP found to be reproducibly associated with heart disease rs2943634 associated with high density lipoprotein (HDL) cholesterol Association studies of 22 candidate SNPs with late-onset Alzheimer's disease. Evaluation of the association of genetic variants on the chromosomal loci 9p21.3, 6q25.1, and 2q36.3 with angiographically characterized coronary artery disease. Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Genome-wide association studies for atherosclerotic vascular disease and its risk factors. Genetics of coronary artery disease: focus on genome-wide association studies. Evaluation of population impact of candidate polymorphisms for coronary heart disease in the Framingham Heart Study Offspri...
1.2x risk of coronary artery disease
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rs599839 and rs4970834 explain about 1% of the variation in circulating LDL-cholesterol levels. 'When we look at this particular genetic variance, of all the cholesterol variation among the population, 1% of it can be attributed to this particular locus,' said Sandhu. 'This is equivalent to more established genes for LDL regulation, particularly APOE.' rs646776 also linked. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins found each minor allele to increase statin effectiveness by 1.3% (rs646776, β=−0.013, s.e.=0.002, P=1.05 × 10−9 and rs12740374, β=−0.013, s.e.=0.002, P=1.05 × 10−9). 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs1746...
Slightly lower odds of developing CHD.
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[PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of LDL-C and apolipoprotein B. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): LDL-C: p = 5.2 x 10 (-15);ApoB: p = 7.0 x 10(-18). Type of association: CO; GN] [OMIM:?] [GWAS:LDL cholesterol]
Magnitude: 2
Frequency: 42.9%
Repute:Bad
References:8
Frequency: 42.9%
Repute:Bad
References:8
1.26x increased risk for heart disease
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rs17228212 is a SNP found to be associated with heart disease by the German MI (Myocardial infarction) Family Study group in two populations. The odds ratio per allele is 1.26 (CI: 1.11-1.44, p=0.0178). rs599839, rs4970834 and rs17228212 associated with non-HDL cholesterol
Normal (higher) HDL %22Good%22 Cholesterol. HDL ('Good') cholesterol actually cleans your arteries and transports cholesterol out of the body, so it is usually good to have higher HDL cholesterol.
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The (T) allele of rs3843763 was associated with risk for lower high-density lipoprotein (HDL) cholesterol plasma levels in 3 independent population samples, including both Caucasians and African-Americans. [PharmGKB:Curated This SNP has been associated with small changes in HDL cholesterol levels. The T allele has been correlated with lower HDL.] [OMIM:PHOSPHOLIPID TRANSFER PROTEIN; PLTP]
associated with higher HDL cholesterol
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C allele is associated with 1.87mg/dl increase in HDL cholesterol (good cholesterol). [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 18q21.1; Reported Gene(s): LIPG; Risk Allele: rs4939883-T); (p-value= 0.000000000000007).This variant is associated with HDL cholesterol.] [GWAS:Cholesterol, total]
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Apolipoprotein E levels in cerebrospinal fluid and the effects of ABCA1 polymorphisms. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Investigation of variants identified in caucasian genome-wide association studies for plasma high-density lipoprotein cholesterol and triglycerides levels in Mexican dyslipidemic study samples. Genome-wide association of lipid-lowering response to statins in combined study populations. Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration. Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC). [PharmGKB:Non-Curated GWAS results: Comm...
Frequency: 10.6%
References:8
References:8
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Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Investigation of variants identified in caucasian genome-wide association studies for plasma high-density lipoprotein cholesterol and triglycerides levels in Mexican dyslipidemic study samples. Genetics and beyond--the transcriptome of human monocytes and disease susceptibility. Exploring genetic determinants of plasma total cholesterol levels and their predictive value in a longitudinal study. Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. [PharmGKB:Non-Curated GW...
Frequency: 11.5%
References:6
References:6
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Babies who are rs11065987(G;G) are about 1.3 times more likely to be born with tetralogy of Fallot (TOF) http://blog.23andme.com/23andme-research/snpwatch/snpwatch-common-genetic-factors-associated-with-blue-babies/ [GWAS:Hematocrit]
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased LDL cholesterol, increased HDL cholesterol and increased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [Pharm...
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per the 23andMe blog, the minor allele of this SNP (A) was associated with increased LDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Common variants at 30 loc...
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[GWAS:Cholesterol, total]
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15,000 individuals. Each copy of the minor T allele of SNP rs2228671 was related to a decrease of LDL-C levels by 0.19 mmol/L (95% confidence interval (CI) [0.13-0.24] mmol/L, p = 1.5x10(-10)) and a significantly lower risk of coronary artery disease (OR per copy of the T allele: 0.82, 95% CI [0.76-0.89], p = 2.1x10(-7)) [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 19p13.2; Reported Gene(s): LDLR; Risk Allele: rs2228671-G); (p-value= 0.00000000000004).This variant is associated with LDL cholesterol.] [OMIM:LOW DENSITY LIPOPROTEIN RECEPTOR; LDLR] [GWAS:Cholesterol, total]
Frequency: 21.2%
References:3
References:3
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[GWAS:Cholesterol, total]
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[GWAS:None]
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[GWAS:Cholesterol, total]
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[GWAS:None]
Frequency: 27.4%
References:6
References:6
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased cholesterol and triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Loci influe...
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[GWAS:Cholesterol, total]
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per the 23andMe blog, the minor allele of this SNP (C) was associated with decreased HDL cholesterol and increased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS result...
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Physiogenomic analysis of weight loss induced by dietary carbohydrate restriction. Physiogenomic comparison of human fat loss in response to diets restrictive of carbohydrate or fat. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Polymorphism in the CETP gene region, HDL cholesterol, and risk of future myocardial infarction: Genomewide analysis among 18 245 initially healthy women from the Women's Genome Health Study. Genetics and beyond--the transcriptome of human monocytes and disease susceptibility. ...
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[GWAS:None]
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[PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of HDL-C and apolipoprotein A1. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): HDL-C: p = 1.3 x 10 (-10);ApoA1: p = 9.0 x 10(-14). Type of association: CO; GN] [OMIM:?] [GWAS:Cholesterol, total]
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news three SNPs that appear to have different effects in men and women rs3846662 rs2304130 rs2083637 journal LDL-Cholesterol minor allele was associated with up to 2.2-fold lower expression Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. The HMG-CoA reductase gene and lipid and lipoprotein levels: the multi-ethnic study of atherosclerosis. Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. Analysis of recently identifie...
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[GWAS:Cholesterol, total]
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http://www.medscape.com/viewarticle/832327 Each additional allele of rs17238484(G) was associated with a mean 0.06-mmol/L lower LDL-cholesterol level. Similar reductions were associated with rs12916 SNP. In addition, they found that each additional allele of rs17238484-G was associated with a higher body weight (0.30 kg), waist circumference (0.32 cm), and plasma insulin concentration (1.62%) and plasma glucose concentration (0.23%). Again, the rs12916 SNP had similar effect [OMIM:?] [GWAS:None]
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[GWAS:Cholesterol, total]
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[GWAS:None]
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sex-specific association of rs261342, rs12593008 and rs8028759 high-density lipoprotein cholesterol
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Molecular population genetics of PCSK9: a signature of recent positive selection. [OMIM:?] [GWAS:None]
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[GWAS:Cholesterol, total]
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Genome-wide association study of plasma polyunsaturated fatty acids in the InCHIANTI Study. Genetic determinants of circulating sphingolipid concentrations in European populations. Single nucleotide polymorphisms in the FADS gene cluster are associated with delta-5 and delta-6 desaturase activities estimated by serum fatty acid ratios. FADS genetic variants and omega-6 polyunsaturated fatty acid metabolism in a homogeneous island population. Genetic variation in lipid desaturases and its impact on the development of human disease. Genetic variation of the FADS1 FADS2 gene cluster and n-6 PUFA composition in erythrocyte membranes in the European Prospective Investigation into Cancer and Nutrition-Potsdam study. FADS1 genetic variability interacts with dietary alpha-linolenic acid intake to ...
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rs1367117 (C711T/711C>T) is a SNP within APOB (Apolipoprotein B). among 97 hypertensive subjects, C allele carriers responded to irbesartan with an average blood pressure reduction of 19 mmHg, however, they did not respond to atenolol associated with apoB levels [PharmGKB:Curated The APOB:711C>T, C allele was associated with reduction of blood pressure in response to irbesartan treatment but not atenolol treatment.] [OMIM:?] [GWAS:None]
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[PharmGKB:Curated In a case-control study of European populations, rs4299376 was found to be associated with risk of gallstones.] [GWAS:None]
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}}per the 23andMe blog, the minor allele of this SNP (T) was associated with increased LDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} Analysis of recently identified dyslipidemia alleles reveals...
Normal B12 levels
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From : We identified a strong association (p = 5.36 x 10(-17)) between rs492602 in the FUT2 gene and plasma vitamin B(12) levels in a genome-wide scan (n = 1,658) and an independent replication sample (n = 1,059) from the Nurses' Health Study. Women homozygous for the rs492602(C) allele (in dbSNP orientation) had higher B(12) levels. This allele is in strong linkage disequilibrium with the FUT2 nonsecretor variant encoding W143X, suggesting a plausible mechanism for altered B(12) absorption and plasma levels. [PharmGKB:Curated GWAS Results: Common variants of FUT2 are associated with plasma vitamin B12 levels (Initial Sample Size: 1,658 women; Replication Sample Size: 1,059 women; Risk Allele: rs492602-G). This variant is associated with Plasma level of vitamin B12.] [OMIM:FUCOSYLTRANSFER...
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[PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 8q24.13; Reported Gene(s): TRIB1; Risk Allele: rs6987702-G); (p-value= 0.000003).This variant is associated with LDL cholesterol.] [GWAS:Cholesterol, total]
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LDL cholesterol and total cholesterol levels being the quantitative trait associated with in [GWAS:Quantitative traits]
Frequency: 52.2%
References:0
References:0
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sex-specific association of rs261342, rs12593008 and rs8028759 high-density lipoprotein cholesterol
elevated lipids
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rs693 increases susceptibility to Elevated Apolipoprotein B and LDL-Cholesterol for carriers of the T allele [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 2p24.1; Reported Gene(s): APOB; Risk Allele: rs693-G); (p-value= 0.00000000000000004).This variant is associated with LDL cholesterol.] [OMIM:APOLIPOPROTEIN B; APOB] [GWAS:Cholesterol, total]
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gwas among adults residing on Korcula Island in Croatia, cholesterol, the G allele associated with increased total cholesterol and increased LDL cholesterol<br><br> [PharmGKB:Non-Curated GWAS results: Genome-wide association study of biochemical traits in Korcula Island, Croatia. (Initial Sample Size: 898 individuals; Replication Sample Size: NR); (Region: 21q22.3; Reported Gene(s): PKNOX1; Risk Allele: rs2839619-G); (p-value= 0.000008).This variant is associated with Biochemical measures.] [GWAS:Biochemical measures]
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[GWAS:None]
Frequency: 58.4%
References:2
References:2
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gwas among adults residing on Korcula Island in Croatia, cholesterol, the C allele associated with decreased total cholesterol levels<br><br> [PharmGKB:Non-Curated GWAS results: Genome-wide association study of biochemical traits in Korcula Island, Croatia. (Initial Sample Size: 898 individuals; Replication Sample Size: NR); (Region: 12q24.23; Reported Gene(s): KSR2; Risk Allele: rs10444502-C); (p-value= 0.000006).This variant is associated with Biochemical measures.] [GWAS:Biochemical measures]
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[GWAS:None]
Frequency: 63.7%
References:7
References:7
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per the 23andMe blog, the minor allele of this SNP (C) was associated with increased cholesterol and triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Loci influe...
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[GWAS:Cholesterol, total]
Frequency: 67.3%
References:1
References:1
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total cholesterol being the quantitative trait associated with in [GWAS:Quantitative traits]
Frequency: 69.0%
References:2
References:2
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gwas among adults residing on Korcula Island in Croatia, cholesterol, the A allele associated with decreased total cholesterol levels<br><br> [PharmGKB:Non-Curated GWAS results: Genome-wide association study of biochemical traits in Korcula Island, Croatia. (Initial Sample Size: 898 individuals; Replication Sample Size: NR); (Region: 12q21.33; Reported Gene(s): Intergenic; Risk Allele: rs10777332-A); (p-value= 0.000005).This variant is associated with Biochemical measures.] [GWAS:Biochemical measures]
Frequency: 75.0%
References:1
References:1
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[GWAS:Cholesterol, total]
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[GWAS:None]
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[GWAS:Cholesterol, total]
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[GWAS:Cholesterol, total]
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rs1169288 (Ile27Leu) is a SNP in located within the HNF1A (Hepatocyte nuclear factor 1 homeobox A) gene. The C allele encodes for the Leu variant. among 356 unrelated Japanese men, lower HDL cholesterol was observed in those with the Ile/Ile genotype (and higher in the Leu/Leu genotype) minor alleles of rs1169288, rs1169286, rs2464196, rs1169310 constitutes a common haplotype (freq. 30%) associated with lower CRP levels [PharmGKB:Curated In a candidate gene-based association analysis of 4333 European-descended, age 65 or older, subjects from the CHS (Cardiovascular Health Study), this was one of the SNPs most strongly associated with plasma C-reactive protein levels. The minor allele is part of a haplotype of frequency 30% which was associated with lower levels of CRP.] [OMIM:INSULIN RESI...
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The T allele of rs1260326 has been associated with type 2 diabetes and hypertriglyceridemia. A fine mapping approach indicates that this SNP, rs1260326, shows the strongest association signal with metabolic phenotypes in the region that also harbors the tightly linked (r(2)=0.93) SNP rs780094, which has been previously associated with triglyceride and glucose concentrations. This SNP, rs1260326, encodes a common missense glucokinase regulatory protein gene GCKR variant. gout association, based on Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. The common P446L polymorphi...
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T allele is associated with 3.47mg/dl increase in HDL cholesterol (good cholesterol). [PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of HDL-C and apolipoprotein A1. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): HDL-C: p = 1.0 x 10 (-41);ApoA1: p = 1.1 x 10(-34). Type of association: CO; GN] [OMIM:?] [GWAS:HDL cholesterol]
common in complete genomics Predicted to be a NAT2 slow metabolizer.
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With 99% sensitivity and 95% specificity, at least in Caucasian populations, rs1495741 is reported to classify the NAT2 phenotype of an individual; it therefore is a candidate to replace the 7-SNP panel used in genosets such as gs138, gs139, and gs140. The rs1495741(A;A), (A;G) and (G;G) genotypes predicted slow, intermediate, and rapid NAT2 acetylation phenotypes, respectively. [GWAS:None]
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Associated with baseline cholesterol levels in a study of 9,000+ individuals in Washington County, Maryland. [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs2016520 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0056 Type of association: PD; CO]
Normal/Average risk for Alzheimer's
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Apolipoprotein E ApoE status is technically defined by two different SNPs, rs429358 and rs7412. This SNP, rs4420638, is situated about 14kb away in the adjacent ApoC1 gene and is co-inherited with ApoE and thus associated with late-onset Alzheimer's disease. rs4420638 (the proxy SNP) is not independent of rs429358. These two SNPs are correlated with each other and it's believed that most of the association with AD at rs4420638 is due to its proximity to rs429358. That said, rs4420638 is not a perfect proxy for rs429358 either -- rs4420638 correlates better for certain genotypes and for certain ethnicities. For example, if you have the genotype at rs4420638 that is more correlated with the e4 allele of APOE, you still only have a 50% chance of actually having the e4 allele. And rs4420638 is...
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per the 23andMe blog, the minor allele of this SNP (T) was associated with decreased HDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} Analysis of recently identified dyslipidemia alleles reveals t...
normal http://www.diygenomics.org/webapp/gen_data.php
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Located close to ApoE4, yet may independently (also) influence risk of Alzheimer's disease. A case-control study of 381 patients found a 2x higher risk for Alzheimer's disease associated with the rarer rs2075650(G) allele. This allele is associated with earlier onset of Alzheimer's disease, by ~7 years. (news) The data from this study are available online at The association of this SNP with late-onset Alzheimer's disease] was confirmed by a study reported in PLoS Genetics. The A allele of this SNP is one of 150 identified as relevant to exceptional longevity in Recent work suggests, however, that the linkage disequilibrium between rs2075650 and the ApoE ε4 defining SNP rs429358 means that there may be little, if any, independent effect of rs2075650 on Alzheimer's risk. rs2075650] was ...
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per the 23andMe blog, the minor allele of this SNP (T) was associated with increased HDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Genome-wide association a...
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per the 23andMe blog, the minor allele of this SNP (T) was associated with decreased cholesterol and increased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: L...
common in complete genomics
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per the 23andMe blog, the minor allele of this SNP (C) was associated with decreased HDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Common variants at 30 loc...
common in complete genomics
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news three SNPs that appear to have different effects in men and women rs3846662 rs2304130 rs2083637 [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 19p13.11; Reported Gene(s): NCAN; Risk Allele: rs2304130-G); (p-value= 0.000003).This variant is associated with LDL cholesterol.] [GWAS:Cholesterol, total]
common on affy axiom data
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased LDL cholesterol, increased HDL, and decreased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Cur...
common in complete genomics
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The 23andMe blog reports that the minor allele of this SNP (A) is associated with decreased LDL levels, increased HDL cholesterol levels, and decreased triglyceride levels. DeCode reports that the G allele is associated with a lower risk of gallstone disease (cholelithiasis) . {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 ...
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y or Cys282Tyr mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who act...
Magnitude: 0
Frequency: 92.9%
Repute:Good
References:8
Frequency: 92.9%
Repute:Good
References:8
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rs12272004 associated with alpha-tocopherol (meta-analysis p = 7.8 x 10(-10)) levels; the association was substantially weaker when adjusted for triglyceride levels (p = 0.002). [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 11q23.3; Reported Gene(s): APOA1, APOA4, APOA5, APOC3; Risk Allele: rs12272004-C); (p-value= 0.0000000000005).This variant is associated with LDL cholesterol.] [GWAS:Cholesterol, total]
common in complete genomics
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per the 23andMe blog, the minor allele of this SNP (T) was associated with decreased HDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Common variants at 30 loc...
common on affy axiom data
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per the 23andMe blog, the minor allele of this SNP (A) was associated with increased LDL cholesterol (wrong allele listed on the 23andMe blog) {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || A || + || || |- |} [PharmGKB:Non-Curat...
common in complete genomics
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sex-specific association of rs261342, rs12593008 and rs8028759 high-density lipoprotein cholesterol Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. [GWAS:Metabolite levels]
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The rs964184(G;G) genotype is associated with hypertriglyceridemia. [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 11q23.3; Reported Gene(s): APOA1, APOC3, APOA4, APOA5; Risk Allele: rs964184-G); (p-value= 0.000000000001).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
common in complete genomics
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total cholesterol being the quantitative trait associated with in [GWAS:Quantitative traits]
1 genoset 73 snps
(hide) Chondrodysplasia
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[OMIM:?]
Magnitude: 0
Frequency: 67.3%
Repute:Good
References:0
Frequency: 67.3%
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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X-linked recessive chondrodysplasia punctata: spectrum of arylsulfatase E gene mutations and expanded clinical variability. [OMIM:CHONDRODYSPLASIA PUNCTATA 1, X-LINKED RECESSIVE]
6 snps
(hide) Chorionic plate inflammation
increased risk for chorionic plate inflammation
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rs1554973 is a SNP near the toll-like receptor 4 TLR4 gene. A study of 109 pregnant women focusing on TLR4 SNPs associated with chorionic plate inflammation concluded that rs1554973 was associated with increased risk when present in the fetal genome. The risk allele's increased odds ratio for clinically significant inflammation was 4.95 (CI: 3.0-5.6, p = .005). No evidence of major effects in several Toll-like receptor gene polymorphisms in rheumatoid arthritis. Traffic-related air pollution, oxidative stress genes, and asthma (ECHRS). Sequence variants in the TLR4 and TLR6-1-10 genes and prostate cancer risk. Results based on pooled analysis from three independent studies. Role of polymorphic variants as genetic modulators of infection in neonatal sepsis. Interaction between interleukin-1...
Frequency: 74.6%
References:18
References:18
normal
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rs10759932 is a SNP in the toll-like receptor 4 TLR4 gene. A study of 109 pregnant women focusing on TLR4 SNPs associated with chorionic plate inflammation concluded that rs10759932 was associated with increased risk when present in the mother's genome. The risk allele's increased odds ratio for clinically significant inflammation was 5.2 (CI: 3.2-6.4, p = .006)
2 snps
(hide) Chronic kidney disease
Magnitude: 1.5
Frequency: 48.7%
Repute:Bad
References:6
Frequency: 48.7%
Repute:Bad
References:6
reported to have some negative associations with kidney function Although it is a fairly common genotype in Caucasians, donor kidneys with this genotype appear to be rejected in transplant cases roughly twice as much as (G;G) donor kidneys.
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rs17319721 is a SNP located in an intron of the SHROOM3 gene on chromosome 4, apparently in the middle of a transcription factor 7–like 2–dependent (TCF7L2-dependent) enhancer element. The rs17319721(A) allele is associated with increased SHROOM3 transcription, and this increased expression may explain both the preliminary reports that this SNP is associated with increased risk for chronic kidney disease (CKD) and with increased odds of kidney transplant rejection, when the (A) allele is present in the donor (allograft) kidney. [GWAS:Renal function and chronic kidney disease]
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
Frequency: 14.2%
References:1
References:1
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[GWAS:Chronic kidney disease]
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This SNP is reportedly associated with chronic kidney disease and kidney stones. [GWAS:None]
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
1.2x increased risk for chronic kidney disease
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rs6495446, an intronic SNP in the MTHFS gene, was associated with increased risk for chronic kidney disease based on a study associated with the Framingham Heart Study of ~1,000 Caucasian individuals. The odds ratio rs6495446(C) allele was 1.24 (CI: 1.09-1.41, p=0.001).news 23andMe reports this same information with a different emphasis: each T allele lowers the odds of chronic kidney disease by 0.8 times.
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
Frequency: 39.8%
References:1
References:1
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
Frequency: 50.0%
References:1
References:1
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
Frequency: 53.8%
References:1
References:1
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
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[GWAS:Chronic kidney disease]
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This SNP, rs653178, is basically a proxy (r<sup>2</sup>>0.99) for rs3184504, as both are associated with celiac disease; see rs3184504 for more details. This SNP is also associated with risk of hypertension. 23andMe blog blood pressure [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 13; CELIAC13] [GWAS:Celiac disease]
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[GWAS:Chronic kidney disease]
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The T allele of rs1260326 has been associated with type 2 diabetes and hypertriglyceridemia. A fine mapping approach indicates that this SNP, rs1260326, shows the strongest association signal with metabolic phenotypes in the region that also harbors the tightly linked (r(2)=0.93) SNP rs780094, which has been previously associated with triglyceride and glucose concentrations. This SNP, rs1260326, encodes a common missense glucokinase regulatory protein gene GCKR variant. gout association, based on Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. The common P446L polymorphi...
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23andMe blog each G at rs4293393 decreased the odds of chronic kidney disease by 24%. Approximately 18% of people with European ancestry have at least one G at this SNP. DeCode reports that the T allele of rs4293393 is associated with kidney stones and chronic kidney disease. This SNP may also be associated with susceptibility to gout], hypertension, and diabetes.
Magnitude: 0
Frequency: 69.8%
Repute:Good
References:8
Frequency: 69.8%
Repute:Good
References:8
Magnitude: 0
Frequency: 84.6%
Repute:Good
References:1
Frequency: 84.6%
Repute:Good
References:1
30 snps
(hide) Chronic obstructive pulmonary disease
Magnitude: 3
Frequency: 15.9%
Repute:Bad
References:102
Frequency: 15.9%
Repute:Bad
References:102
higher risk for nicotine dependence, lower risk for cocaine dependence
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Associated with smoking phenotype (p=0.007) based on association study of 2,000+ individuals, and functional studies demonstrated that the risk allele decreased response to a nicotine agonist, therefore the rs16969968(A) allele is likely to be involved in nicotine dependence. In a study 500+ individuals with cocaine dependence, the same rs16969968(A) allele was associated with a 0.67x decreased risk (p = 0.0045). A study of 200 individuals replicated the association between this SNP and nicotine dependence, and also concluded that the rs16969968(A) allele was significantly associated with 'enhanced pleasurable responses' to a person's first cigarette. 23andMe blog 23andMe considers rs1051730 equivalent The association between rs16969968 and lung cancer may, in part, be confounded by chroni...
1.80x lung cancer risk; decreased response to alcohol
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23andMe blog rs8034191(C;C) decreased response to alcohol rs8034191 increases susceptibility to Lung cancer 1.27 times for heterozygotes (CT) and 1.80 times for homozygotes (CC) rs8034191 increases susceptibility to Lung cancer 1.28 times for heterozygotes (CT) and 1.81 times for homozygotes (CC) [PharmGKB:Non-Curated GWAS results: Familial Aggregation of Common Sequence Variants on 15q24-25.1 in Lung Cancer. (Initial Sample Size: 194 cases, 219 controls; Replication Sample Size: 3,878 cases, 4,831 controls); (Region: 15q25.1; Reported Gene(s): LOC123688, PSMA4, CHRNA3, CHRNA5, CHRNB4; Risk Allele: rs8034191-G); (p-value= 0.00000001).This variant is associated with Lung cancer.] [OMIM:LUNG CANCER SUSCEPTIBILITY 2; LNCR2] [GWAS:Lung cancer] [GWAS:Lung cancer]
1.8x increased risk of lung cancer; reduced response to alcohol, therefore possibly increased risk of alcohol abuse
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rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...
if a smoker, somewhat more likely to develop COPD if a smoker, somewhat more likely to develop COPD
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rs543749, also known as IVS21_22 or V-1, is a SNP in the ADAM metallopeptidase domain 33 ADAM33 gene. A study of ~600 non-Hispanic white males who smoked concluded that rs543749(G;G) carriers, i.e. those homozygous for the most common allele, were more likely (p< 0.0026, after Bonferroni correction) to develop chronic obstructive pulmonary disease (COPD) than carriers of one or two rs543749(T) alleles.
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Formerly known as the very well studied rs1982073 [PharmGKB:Curated In conjunction with polymorphism at codon 25, defines high-, medium- or low-producer haplotype; Pro allele has been associated with higher levels of circulating TGFB1; Cystic Fibrosis patients who are C homozygotes may have increased risk of severe pulmonary disease; association found of C allele with increased risk of invasive breast cancer; associated with bone mineral density and genetic susceptibility to osteoporosis in Japanese adolescents and postmenopausal women; C allele may be involved in development of EBV-related diseases;C allele associated with increased risk for esophageal squamous cell carcinoma in Chinese; T allele associated with familial vesicoureteral reflux; C allele associated with increased severity ...
0.44x decreased risk for chronic obstructive pulmonary lung disease
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rs3736309 is a SNP in the aquaporin 5 (AQP5) gene. Among other roles, the aquaporin proteins play a critical role in the maintenance of normal lung water homeostasis. A study of 332 Chinese Han Chronic obstructive pulmonary disease (COPD) patients and 373 unrelated, age-matched controls concluded that carriers of a rs3736309(G) allele had a lower risk of COPD than rs3736309(A;A) carriers, with an odds ratio of 0.44 (CI: 0.307-0.631).
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Preliminary demonstration of an allelic association of the IREB2 gene with Alzheimer's disease. Chromosome 15q25.1 genetic markers associated with level of response to alcohol in humans. Integration of genomic and genetic approaches implicates IREB2 as a COPD susceptibility gene. The role of IREB2 and transforming growth factor beta-1 genetic variants in COPD: a replication case-control study. [GWAS:Chronic obstructive pulmonary disease]
Frequency: 44.2%
References:4
References:4
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[GWAS:Chronic obstructive pulmonary disease]
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A study of 414 (ex)-smokers older than 50 years concluded that vitamin D levels were reduced by 25% in rs7041](T;T) homozygotes (p<0.0001), and even after correction for age, gender and smoking history, they were also at increased risk for chronic obstructive pulmonary disease (COPD; odds ratio 2.11, CI: 1.20-3.71, p=0.009). They conclude that since vitamin D deficiency occurs frequently in COPD and correlates with its severity, vitamin D supplementation may be warranted in patients with severe COPD, and especially in those carrying rs7041(T) alleles. [OMIM:?] [GWAS:Serum vitamin D-binding protein levels]
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Individual and cumulative effects of GWAS susceptibility loci in lung cancer: associations after sub-phenotyping for COPD. [OMIM:?] [GWAS:Chronic obstructive pulmonary disease]
lower TGF-β1 levels, higher risk for COPD? This normal C version significantly reduces TGF-β1 levels by allowing AP1 to downregulate TGF-β1 production.
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rs1800469, also known as -509 C>T or −1347 C > T, is an SNP in the promoter region of the transforming growth factor beta1 TGFB1 gene. That means it doesn't change the nature of the TGF-β1 protein, but it does change the amount produced. The T version increases the amount of TGF-β1 produced, by preventing AP1 from binding to this region where in the C version it would normally downregulate production. That increased TGF-β1 production with the T version is probably what causes all the health effects of this SNP. Whether increased TGF-β1 is good or bad probably depends on the disease you are interested in. It has been associated with increased risk for chronic obstructive pulmonary disease (COPD). Although smoking is the main risk factor, smokers with a rs1800469(C) allele (or 2 other ...
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rs3847987 in the vitamin D pathway was associated with the time to onset of COPD. The SNP is a cytosine-to-adenine switch, and men with two copies of the adenine variant were more likely to develop COPD. The hazard ratio was 1.60, with a 95% confidence interval from 1.26 to 2.05, which was significant at P=0.005. news
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In a study of 389 non-Hispanic Caucasian patients with chronic obstructive pulmonary disease (COPD), rs3024791 was associated with exacerbations, which are defined as COPD-related emergency room visits.
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
common in complete genomics
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rs1009668 was significantly (p = 0.04) associated with bronchodilator responsiveness among patients with severe chronic obstructive pulmonary disease
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asthma related This SNP is in the promoter region of the IL-13 gene PMID: 17615386 IL-13 is involved in pulmonary inflammation, remodeling and susceptibility to chronic obstructive pulmonary disease (COPD). This IL13 promoter polymorphism may modulate the adverse effects of cigarette smoking on pulmonary function in long-term cigarette smokers. Every 20 pack-year increment in smoking was associated with a 2.4% reduction in mean ppFEV1(forced expiratory volume in 1 second, a measure used to assess lung disease, like COPD) in the common homozygous (CC) or heterozygous (CT) promoter genotypes, and an 8.2% reduction in mean ppFEV1 in minor allele homozygotes (TT, recessive model). *pack-year= packs per day x years smoked rs1800925 and/or rs11568506 related to psoriasis and/or Crohn's disease ?...
better response to inhaled corticosteroid in patients with COPD
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rs242941 is a SNP in the corticotrophin-releasing hormone receptor 1 CRHR1 gene. (G;G) better response to inhaled corticosteroids fluticasone propionate and salmeterol in patients with COPD in a Korean study with 84 subjects. [PharmGKB:Curated Haplotype tagging SNP.]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
common in complete genomics
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rs28929474, also known as Glu342Lys as well as E366K, is a SNP in the serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 SERPINA1 gene. This SNP is the one most frequently leading, when homozygous, to the complications of alpha-1 antitrypsin deficiency and the associated high risk of emphysema and liver disease. Between 1 - 2% of US Caucasians are thought to be (heterozygous) carriers for this SNP, leading some associations, like the Alpha-1 Foundation, to call for mass carrier screening. * 23andMe blog rs28929474(T) increases odds of liver disease in cystic fibrosis patients by 4.17 times. (T;T) at both copies of this SNP causes alpha-1 antitrypsin deficiency; note use of opposite strand nomenclature by this company. Genetic polymorphisms and susceptibilit...
common in complete genomics
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rs17580, also known as the S or PiS allele, is a SNP in the SERPINA1 gene. Levels of alpha-1 antitrypsin (encoded by the SERPINA1 gene) may be reduced in carriers of the rs17580(T) allele, but there is no known association with liver disease or cystic fibrosis. The rs17580 PiS variant is most associated with risk of developing COPD, especially in smokers, but it's association with emphysema is variable. See rs28929474 for the most common pathologic SNP (PiZ) in the SERPINA1 gene. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is T, but test results may be in the plus orientation where the risk allele is A (although currently 23andMe reports the risk allele as T). This SNP has an ambiguous flip which can make...
19 snps
(hide) Cleft palate
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rs910586, rs2819861, and rs1934328 may influence cleft palate
Normal risk of cleft lip
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risk of cleft lip 23andMe considers rs861020 a proxy Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 Genome scan, fine-mapping, and candidate gene analysis of non-syndromic cleft lip with or without cleft palate reveals phenotype-specific differences in linkage and association results. Lack of association between IRF6 polymorphisms (rs2235371 and rs642961) and non-syndromic cleft lip and/or palate in a Brazilian population. Current concepts in genetics of nonsyndromic clefts. Studies of palatine rugae and interferon regulatory factor 6 variations in a group of families with sporadic hypodontia. IRF6 gene variants in Central European patients with non-syndromic cleft lip with or without cleft palate. Family-based study sh...
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
normal
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A genome-wide association study involving 224 cases and 383 controls of Central European origin found that significant association between rs987525 and risk for nonsyndromic cleft lip with or without cleft palate (NSCL/P). The odds ratio for rs987525(A;G) individuals was 2.57 (CI: 2.02-3.26), and for rs987525(A;A), 6.05 (CI: 3.88-9.43). The calculated population attributable fraction for this marker is 0.41, suggesting that this study has identified a major genetic cause for NSCL/P. 23andMe blog article Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 Family-based study shows heterogeneity of a susceptibility locus on chromosome 8q24 for nonsyndromic cleft lip and palate. Association between genetic variants of reported c...
4 snps
(hide) Cluster headaches
2-6x increased risk for cluster headaches
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rs2653349, also known as G1246A, is a SNP in the HCRTR2 hypocretin-orexin gene. It has been linked primarily to cluster headaches. The more common allele (G) has been linked to increased risk; alternatively, this could be seen as implying that the less common (A) allele reduces cluster headache risk. In the (first) study, 100+ Italian patients were analyzed to reveal that rs2653349(G;G) genotypes were at 5x increased risk for the disorder, compared with (A;G) and (A;A) genotypes. A study of 200+ German patients indicated that (G;G) homozygotes were at 2x increased risk (CI: 1.32-2.92, p = 0.0007) for cluster headaches. A meta-analysis of 3 pooled studies concluded that the rs2653349(G;G) genotype showed a higher disease risk compared to the remaining genotypes (odds ratio 1.69, CI:1.11-2.5...
1 snp
(hide) Colon cancer
1.6x increased risk for prostate cancer; also other cancers 1.4 times as likely to develop colorectal cancer
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. This SNP has also been reported to influence the cancer-risk-decreasing effect of aspirin. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neig...
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appears relevant to colon cancer rs334348, rs334349 and rs1590 (in total linkage disequilibrium with each other) and a fourth marker, rs7871490
normal
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rs2167270 is a SNP in the leptin LEP gene. In a study of ~1,500 colon cancer patients, the rs2167270(A;A) genotype was underrepresented, leading to an odds ratio of 0.79 (CI: 0.64-0.98). Common variants in the 5' region of the leptin gene are associated with body mass index in men from the National Heart, Lung, and Blood Institute Family Heart Study. Adipokine genes and prostate cancer risk. Leptin is associated with blood pressure and hypertension in women from the National Heart, Lung, and Blood Institute Family Heart Study. Association of maternally inherited GNAS alleles with African-American male birth weight. Lack of association between LEP rs2167270 (19 G>A) polymorphism and disease susceptibility and cardiovascular disease in patients with rheumatoid arthritis.
normal
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rs2308327, also known as K178R, is a SNP in the MGMT gene. The more common allele, rs2308327(A), encodes a lysine (K) at codon 178, while the (G) allele encodes an arginine (R). In a pooled analysis of 200+ lung cancer patients, the rs2308327(G) allele was reported to provide a protective effect against lung cancer, and furthermore, more (G) alleles meant more protection, particularly for smokers. The odds ratios reported (p=0.003) were 0.67 (CI: 0.45-1.01) for heterozygotes, and 0.10 (CI: 0.01-0.94) for rs2308327(G;G) homozygotes. In a study of 300+ colon cancer cases, rs2308327(G), in linkage disequilibrium with the previously reported MGMT Ile(143)Val rs2308321 SNP, had an inverse association with colorectal cancer risk (odds ratio 0.52, CI: 0.35-0.78, unadjusted p(trend) = 0.0003 for t...
common in clinvar
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rs2020912 is a SNP in the MSH6 gene on chromosome 2, which (as a gene) has been associated with hereditary nonpolyposis colorectal cancer (HNPCC). It is not clear whether this variant predisposes individuals to cancers such as colorectal cancer. In ClinVar, some entries list it as pathogenic, most list it as benign, and one lists it as likely to be benign. Even so, this variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 600678.0006 [OMIM:?]
common in complete genomics common for Caucasians on the 23andme platform
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also known as rs28933380 related to colorectal cancer, FAMILIAL, Ashkenazi The APC I1307K mutation is primarily found in people of Ashkenazi Jewish heritage (Jews of Eastern European or Russian ancestry). Researchers believe that 6% of Ashkenazi Jews carry this gene mutation, making them at a significantly higher risk for developing colorectal cancer. It is also found among Sephardi and Mizrahi Jews and Muslim and Christian Palestinian Arabs, as well as Negev Bedouin. Many patients with colorectal cancer experience no symptoms in the early stages. In fact, symptoms may not appear until the disease is in advanced stage. Routine colorectal screening is very important. Even children from 11 years of age should be screened if there is a family history of colorectal cancer. * APC I1307K and Col...
6 snps
(hide) Colorblind
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colorblindness
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colorblindness
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
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colorblindness
3 snps
(hide) Colorectal cancer
1.6x increased risk for prostate cancer; also other cancers 1.4 times as likely to develop colorectal cancer
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. This SNP has also been reported to influence the cancer-risk-decreasing effect of aspirin. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neig...
A1/A2: Bad at avoidance of errors. 0.5x lower OCD risk, 0.87x lower Tardive Diskinesia risk, higher ADHD risk. More Alcohol Dependence. Lower risk of Postoperative Nausea. Increased obesity. Bupropion is not effective. The DRD2 TaqIA A1/A2 version causes less dopamine receptors. Doesn't learn from mistakes well. Reduced response to errors and increased addictive behavior Men may have half the risk of Obsessive Compulsive Disorder but higher risk of ADHD. Women have lower Persistence. 0.87x reduced risk of Tardive Diskinesia when taking dopamine receptor antagonists. Slightly increased risk of alcoholism and smoking addiction. Slower recovery from traumatic brain injury. Lower risk of postoperative nausea within 6 hours of surgery. Bupropion (Wellbutrin, Budeprion, Prexaton, Elontril, Aple...
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain . Reduced response to errors and increased addictive behavior It has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessa...
Magnitude: 2
Frequency: 21.2%
Repute:Bad
References:26
Frequency: 21.2%
Repute:Bad
References:26
slight (~1.5x) increase in colorectal cancer risk see discussion at rs16892766
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rs16892766 on 8q23.3 (colorectal cancer OR 1.88, CI: 1.30–2.72, P=0.0007) [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies colorectal cancer susceptibility loci on chromosome 10p14 and 8q23.3 (Initial Sample Size: 922 cases, 927 controls; Replication Sample Size: 17,872 cases, 17,526 controls; Risk Allele: rs16892766-A).] [OMIM:COLORECTAL CANCER, SUSCEPTIBILITY TO, 6; CRCS6] [GWAS:None] [GWAS:Colorectal cancer]
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
Normal (lower) risk of Type 2 Diabetes and Gestational Diabetes. Normal insulin secretion in the pancreas. This has been confirmed in most races.
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This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). This SNP is also known as IVS3C>T. rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. Full text of the paper is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse population Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion...
1x risk for colorectal cancer
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rs4939827 is one of 3 SNPs in the SMAD7 gene associated with risk for colorectal cancer, based on a large study (7,400+ cases) conducted in the UK. The odds ratios show a decreased risk for the minor rs4939827(C) allele; the OR for (C;C) homozygotes is 0.73 (CI: 0.66-0.8), and for (C;T) heterozygotes 0.86 (CI: 0.79-0.92), overall p=1x10<sup>-12</sup>. [PharmGKB:Non-Curated GWAS Results: Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21 (Initial Sample Size: 981 cases, 1,002 controls; Replication Sample Size: 16,476 cases, 15,351 controls; Risk Allele: rs4939827-T).] [OMIM:MOTHERS AGAINST DECAPENTAPLEGIC, DROSOPHILA, HOMOLOG OF, 7; SMAD7] [GWAS:Colorectal cancer] [GWAS:Colorectal cancer]
complex; generally greater risk for cancer progression
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rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and H131R. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...
1.17x increased risk of colorectal cancer
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rs3802842 is a SNP in a region of ch 11q23.1 that has been associated with some cancers. IN a study of over 10,000 cases of colorectal cancer, rs3802842(C) was associated with increased risk (odds ratio 1.17, CI: 1.12-1.22, p = 1.08 x 10e-12). Additional SNPs in chromosomal regions 8q21, 8q24, 10p14, 11q, 15q13.3 and 18q21 can be combined additively to produce an overall risk, with an average odds ratio per risk allele of 1.19. [PharmGKB:Non-Curated GWAS Results: Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21 (Initial Sample Size: 981 cases, 1,002 controls; Replication Sample Size: 16,476 cases, 15,351 controls; Risk Allele: rs3802842-C).] [OMIM:COLORECTAL CANCER, SUSCEPTIBILITY TO, 7; CRCS7] [GWAS:None]...
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This SNP is part of a haplotype reported for the KLRK1 gene, potentially associated with risk for colorectal cancer; see details at rs1049174. [GWAS:Behcet's disease]
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Part of a haplotype Gs286, standalone effect for endometrial cancer is ambiguous. In , no evidence for linkage to colorectal cancer in women was found in a study with 158 European subjects and 563 controls. Genetic variation in sex-steroid receptors and synthesizing enzymes and colorectal cancer risk in women. Catalog of 668 SNPs detected among 31 genes encoding potential drug targets on the cell surface An Epidemiologic Study of Genetic Variation in Hormonal Pathways in Relation to the Effect of Hormone Replacement Therapy on Breast Cancer Risk [GWAS:Endometrial cancer]
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colorectal cancer rs10505477 and rs6983267 yielded allelic p-values of 1.42 x 10(-7) and 2.57 x 10(-7), respectively with OR=1.50 (95% CI: 1.29-1.75). Risk region was delineated by SNPs rs10505477 and rs7014346 and comprised 17 kb [PharmGKB:Non-Curated GWAS Results: Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21 (Initial Sample Size: 981 cases, 1,002 controls; Replication Sample Size: 16,476 cases, 15,351 controls; Risk Allele: rs7014346-A).] [OMIM:COLORECTAL CANCER, SUSCEPTIBILITY TO, 2; CRCS2] [GWAS:Colorectal cancer]
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[GWAS:Colorectal cancer]
Frequency: 15.0%
Repute:Bad
References:17
Repute:Bad
References:17
1x normal risk for colorectal cancer
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rs12953717 is one of 3 SNPs in the SMAD7 gene associated with risk for colorectal cancer, based on a large study (7,400+ cases) conducted in the UK. The odds ratios show an increased risk for the minor rs12953717(T) allele; the OR for (T;T) homozygotes is 1.37 (CI: 1.25-1.5), and for (C;T) heterozygotes 1.11 (CI: 1.03-1.2), overall p=9x10<sup>-12</sup>.
Frequency: 16.8%
References:15
References:15
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nature colorectal cancer rs10411210 RHPN2; P = 4.6 times 10-9) In a replication study of ~1,800 Swedish patients, the rs10411210(T) allele was specifically also shown to be associated with younger age of onset for colorectal cancer. Correcting 'winner's curse' in odds ratios from genomewide association findings for major complex human diseases. Low-penetrance susceptibility variants in familial colorectal cancer. Generalizability and epidemiologic characterization of eleven colorectal cancer GWAS hits in multiple populations. Systematic search for enhancer elements and somatic allelic imbalance at seven low-penetrance colorectal cancer predisposition loci. Relationship between 16 susceptibility loci and colorectal cancer phenotype in 3146 patients. Susceptibility genetic variants associate...
Frequency: 19.5%
References:25
References:25
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Associated with risk of colorectal cancer; (P = 0.005) colorectal cancer rs10505477 and rs6983267 yielded allelic p-values of 1.42 x 10(-7) and 2.57 x 10(-7), respectively with OR=1.50 (95% CI: 1.29-1.75). Risk region was delineated by SNPs rs10505477 and rs7014346 and comprised 17 kb [PharmGKB:Non-Curated GWAS Results: Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24 (Initial Sample Size: 1,257 cases, 1,336 controls; Replication Sample Size: 6,223 cases, 6,443 controls; Risk Allele: rs10505477-A).] [OMIM:COLORECTAL CANCER, SUSCEPTIBILITY TO, 2; CRCS2] [GWAS:Prostate cancer (early onset)] [GWAS:Colorectal cancer]
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[GWAS:Colorectal cancer]
Frequency: 23.0%
References:1
References:1
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[GWAS:Colorectal cancer]
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colorectal cancer (-93G>A, rs1800734) 1,518 patients with CRC, homozygosity for the MLH1 -93A variant was associated with a significantly increased 3-fold risk of CRC negative for MLH1 protein by immunohistochemistry (odds ratio (OR): AA vs GG = 3.30, 95% CI 1.46-7.47, n = 1392, p = 0.004, MLH1 negative vs MLH1 positive CRC) and with a 68% excess of proximal CRC (OR: AA vs GG=1.68, 95% confidence interval (CI) 1.00-2.83, n = 1,518, p = 0.05, proximal vs distal CRC) [PharmGKB:Curated This promoter variant is a risk allele for the development of cancer after methylating chemotherapy for Hodgkin lymphoma.] [OMIM:MutL, E. COLI, HOMOLOG OF, 1; MLH1]
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[GWAS:Colorectal cancer]
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[GWAS:Colorectal cancer]
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nature colorectal cancer rs961253; P = 2.0 times 10-10 [PharmGKB:Curated GWAS results: Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. (Initial Sample Size: 1,902 cases, 1,929 controls; Replication Sample Size: 4,878 cases, 4,914 controls); (Region: 20p12.3; Reported Gene(s): Intergenic; Risk Allele: rs961253-A); (p-value= 0.0000000002).This variant is associated with Colorectal cancer.] [OMIM:COLORECTAL CANCER, SUSCEPTIBILITY TO, 11; CRCS11] [GWAS:Colorectal cancer]
Frequency: 38.9%
References:5
References:5
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[GWAS:Colorectal cancer]
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[GWAS:Colorectal cancer]
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colorectal cancer survival rs863221, located in MSH3 (HR: 0.59, 95% confidence interval (CI) 0.42-0.82, p-value: 0.001)
Frequency: 41.1%
References:2
References:2
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[GWAS:Colorectal cancer]
Frequency: 41.6%
References:1
References:1
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[GWAS:Colorectal cancer]
common; higher LDL-C and total cholesterol
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rs174537 is a SNP near the FADS1 gene on chromosome 11. The FADS1 gene is one of 3 fatty acid desaturases in this region; higher polyunsaturated fatty acids (PUFA) levels are generally correlated with lower risk for heart disease. A study of 1,075 participants in the InCHIANTI study on aging concluded that rs174537(T;T) individuals had lower arachidonic acid (AA), as well as lower levels of all other polyunsaturates measured (excepting linoleic acid, which followed the opposite pattern, and alpha-linoleic acid), compared to (G;G) homozgyotes (p = 6 x 10e-46), and that this one SNP accounted for almost 19% of the variance in AA levels. Individuals carrying at least one rs174537(G) allele had higher low-density lipoprotein (LDL-C) and total cholesterol levels. This effect of rs174537 was con...
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[GWAS:Colorectal cancer]
Frequency: 44.6%
References:30
References:30
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rs10795668 is a SNP within chromosomal region 10p14. It has been reported in several publications as being associated with higher risk for colorectal cancer. In a replication study of ~1,800 Swedish patients, the rs10795668(G) allele was specifically also shown to be associated with younger age of onset for colorectal cancer and with sporadic cases. Note that this conflicts with the earlier GWAS reports concluding that the risk allele is rs10795668(A). [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies colorectal cancer susceptibility loci on chromosome 10p14 and 8q23.3 (Initial Sample Size: 922 cases, 927 controls; Replication Sample Size: 17,872 cases, 17,526 controls; Risk Allele: rs10795668-A).] [OMIM:COLORECTAL CANCER, SUSCEPTIBILITY TO, 5; CRCS5] [GWAS:Co...
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nature colorectal cancer rs9929218, CDH1; P = 1.2 times 10-8) [PharmGKB:Curated GWAS results: Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. (Initial Sample Size: 1,902 cases, 1,929 controls; Replication Sample Size: 4,878 cases, 4,914 controls); (Region: 16q22.1; Reported Gene(s): CDH1; Risk Allele: rs9929218-A); (p-value= 0.00000001).This variant is associated with Colorectal cancer.] [OMIM:COLORECTAL CANCER, SUSCEPTIBILITY TO, 9; CRCS9] [GWAS:Colorectal cancer]
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nature colorectal cancer rs4444235, BMP4; P = 8.1 times 10-10) [PharmGKB:Curated GWAS results: Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. (Initial Sample Size: 1,902 cases, 1,929 controls; Replication Sample Size: 4,878 cases, 4,914 controls); (Region: 14q22.2; Reported Gene(s): BMP4; Risk Allele: rs4444235-C); (p-value= 0.0000000008).This variant is associated with Colorectal cancer.] [OMIM:COLORECTAL CANCER, SUSCEPTIBILITY TO, 8; CRCS8] [GWAS:Colorectal cancer]
0.68x decreased risk for bladder cancer
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rs5275, also known as exon1-+837T>C, is a SNP in the PTGS2 gene. A study of 635 Caucasian bladder cancer patients found a reduced risk associated with the minor (C) allele of rs5275, (odds ratio 0.68, CI: 0.54-0.87, p=0.002, remaining significant after multiple comparison adjustment). (T;T) genotype of PTGS2 8473T>C (rs5275) was significantly correlated with a better survival when compared to the combined T/C and C/C genotype (Hazard ratio [HR] = 0.47; P value = 0.046 and HR = 0.16; P = 0.013, respectively) in colorectal cancer Allellic variants in regulatory regions of cyclooxygenase-2: association with advanced colorectal adenoma. Association of frequent consumption of fatty fish with prostate cancer risk is modified by COX-2 polymorphism. Cyclooxygenase-2 polymorphisms in Parkinso...
Normal risk for colorectal cancer
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rs4464148 is one of 3 SNPs in the SMAD7 gene associated with risk for colorectal cancer, based on a large study (7,400+ cases) conducted in the UK. The odds ratios show an increased risk for the minor rs4464148(C) allele; the OR for (C;C) homozygotes is 1.35 (CI: 1.2-1.51), and for (C;T) heterozygotes 1.10 (CI: 1.09-1.21), overall p=7x10<sup>-8</sup>.
lower TGF-β1 levels, higher risk for COPD? This normal C version significantly reduces TGF-β1 levels by allowing AP1 to downregulate TGF-β1 production.
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rs1800469, also known as -509 C>T or −1347 C > T, is an SNP in the promoter region of the transforming growth factor beta1 TGFB1 gene. That means it doesn't change the nature of the TGF-β1 protein, but it does change the amount produced. The T version increases the amount of TGF-β1 produced, by preventing AP1 from binding to this region where in the C version it would normally downregulate production. That increased TGF-β1 production with the T version is probably what causes all the health effects of this SNP. Whether increased TGF-β1 is good or bad probably depends on the disease you are interested in. It has been associated with increased risk for chronic obstructive pulmonary disease (COPD). Although smoking is the main risk factor, smokers with a rs1800469(C) allele (or 2 other ...
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[GWAS:None]
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[GWAS:Colorectal cancer]
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The rs2665802(A;A) genotype was associated with reduced risk of colorectal cancer only among physically inactive individuals, with an odds ratio of 0.76 (CI: 0.52-0.98), and the same genotype was marginally associated with increased risk among individuals who reported physical activity (odds ratio 1.38, CI: 0.98-1.94).
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Part of a haplotype Gs286, standalone effect for endometrial cancer is ambiguous. ''p''-values account for ethnic heterogenity of study population. In , no evidence for linkage to colorectal cancer in women was found in a study with 158 European subjects and 563 controls. Genetic variation in sex-steroid receptors and synthesizing enzymes and colorectal cancer risk in women. [GWAS:Endometrial cancer]
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rs3834129 is a SNP in the CASP8 gene that is also known as the -652 6N ins/del promoter variant. It has been linked to higher risk for multiple tumours including colorectal cancer (CRC) in Chinese populations; however, it showed no association with colorectal cancer risk in a study of 4,000 UK cases. This page demonstrates a bug in User:SNPediaBot. It incorrectly assigned the genotype, probably because it is multiple letters. This makes a good test case. [OMIM:CASPASE 8, APOPTOSIS-RELATED CYSTEINE PROTEASE; CASP8]
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This SNP is part of a haplotype reported for the KLRK1 gene, potentially associated with risk for colorectal cancer; see details at rs1049174.
normal
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rs719725 is a SNP on chromosome 9p24 that has been associated with increased risk of colorectal cancer, based on a study of 1,567 sibships from the Colon Cancer Family Registry. By genotypes, the observed risks were as follows: (A;A) versus (C;C): odds ratios, 1.46, CI: 1.06-2.02; (A;C) versus (C;C): odds ratio 1.50, CI: 1.14-1.98; p = 0.011) : gave an overall meta-analysis (n=17) OR of 1.07 (95% CI 1.03-1.12, p-trend 0.001).
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influences mitosis associated with cancer * breast cancer * colorectal cancer * gastric cancer
average
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rs2306536, a SNP in the CHFR gene, was found to be significantly associated with a lower risk of colorectal cancer (odd ratio 0.53, CI: 0.30-0.94), and to be significantly correlated with the absence of distant metastases, in a case/control study of ~500 Korean patients.
normal
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rs2308327, also known as K178R, is a SNP in the MGMT gene. The more common allele, rs2308327(A), encodes a lysine (K) at codon 178, while the (G) allele encodes an arginine (R). In a pooled analysis of 200+ lung cancer patients, the rs2308327(G) allele was reported to provide a protective effect against lung cancer, and furthermore, more (G) alleles meant more protection, particularly for smokers. The odds ratios reported (p=0.003) were 0.67 (CI: 0.45-1.01) for heterozygotes, and 0.10 (CI: 0.01-0.94) for rs2308327(G;G) homozygotes. In a study of 300+ colon cancer cases, rs2308327(G), in linkage disequilibrium with the previously reported MGMT Ile(143)Val rs2308321 SNP, had an inverse association with colorectal cancer risk (odds ratio 0.52, CI: 0.35-0.78, unadjusted p(trend) = 0.0003 for t...
average
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A study of 7000+ UK patients with colorectal cancer identified two SNPs that increase disease risk, one of which is rs4779584. Inheriting the rs4779584(T) risk allele is estimated to increase overall risk odds by 1.26x (CI: 1.19-1.34, p=4x10e-14). When analyzing data between genotypes, the odds ratios reported for heterozygotes was 1.23x (CI:1.13-1.33), and for rs4779584(T;T) homozygotes, 1.70 (CI: 1.41-2.04). Inheriting the risk variant at both SNP loci (i.e. rs4779584 and rs6983267) is estimated to increase the overall risk of developing colorectal cancer about 3 fold. The authors of this study are quoted as saying that 'the lifetime risk [of bowel cancer] is about 5% in the UK so it's going up to 7% or so if you've got both bad copies of a variant.' nature This SNP has also been associa...
normal
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The INSR A-603G promoter rs1864010 SNP, which is located within a known Sp1-binding site, was associated with the risk of colorectal cancer, with carriers of the G allele having a decreased risk (odds ratios (OR) 0.71, 95% confidence interval (CI) 0.54-0.93). Carrying the variant allele of the IRS1 Gly972Arg rs1801278 SNP further decreased the risk among the INSR-603G allele carriers (OR 0.28, 95% CI 0.11-0.70) multiple myeloma *rs1801278 [C/T versus C/C genotypes; OR, 4.3; 95% confidence interval (CI), 1.5-12.1] *rs6684439 (T/T versus C/C; OR, 2.9; 95% CI, 1.2-7.0) *rs7529229 (C/C versus T/T; OR, 2.5; 95% CI, 1.1-6.0) *rs8192284 (C/C versus A/A; OR, 2.5, 95% CI, 1.1-6.0)
normal
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rs4986790, a SNP also known as Asp299Gly (and also 896A/G) in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in th...
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
common in clinvar
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This SNP, a variant in the CHEK2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C). rs17879961 one of 3 SNPs associated with increased risk of lung cancer [OMIM:?] [GWAS:Lung cancer]
Magnitude: 0
References:0
References:0
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The A allele of this SNP is associated with autosomal recessive Polycystic Kidney disease, but it may also be protective against colorectal cancer. [OMIM:POLYCYSTIC KIDNEY DISEASE, AUTOSOMAL RECESSIVE]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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rs34612342, also known as Tyr179Cys, is one of the two most common pathogenic mutations in the MUTYH gene. The normal allele, encoding the tyrosine, is rs34612342(A), while rs34612342(G) is the risk allele. [Mutation nomenclature according to Genbank accession number NM_001128425.1 c.536A>G, p.Tyr179Cys; alternative numbering can lead to this SNP also being called Tyr151Cys, Tyr152Cys, Tyr165Cys, or Tyr176Cys.] Germline bi-allelic mutations in the MUTYH gene increase the risk of developing multiple adenomatous polyps and colorectal cancer. [OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
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rs36053993, also known as Gly396Asp, is one of the two most common pathogenic mutations in the MUTYH gene. The risk allele is rs36053993(A), as oriented in accordance with dbSNP. (Mutation nomenclature according to Genbank accession number NM_001128425.1 c.1187G>A, p.Gly396Asp; numbering differences can lead to alternative designations including Gly368Asp, Gly369Asp, Gly382Asp, or Gly393Asp.) People with two copies of a single mutation in the MUTYH gene are at higher risk of developing multiple adenomatous polyps and colorectal cancer. [OMIM:?]
common in complete genomics common for Caucasians on the 23andme platform
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also known as rs28933380 related to colorectal cancer, FAMILIAL, Ashkenazi The APC I1307K mutation is primarily found in people of Ashkenazi Jewish heritage (Jews of Eastern European or Russian ancestry). Researchers believe that 6% of Ashkenazi Jews carry this gene mutation, making them at a significantly higher risk for developing colorectal cancer. It is also found among Sephardi and Mizrahi Jews and Muslim and Christian Palestinian Arabs, as well as Negev Bedouin. Many patients with colorectal cancer experience no symptoms in the early stages. In fact, symptoms may not appear until the disease is in advanced stage. Routine colorectal screening is very important. Even children from 11 years of age should be screened if there is a family history of colorectal cancer. * APC I1307K and Col...
normal
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rs266729 is a SNP in the adiponectin ADIPOQ gene that may help elucidate correlations between obesity and some types of cancer. Two case-control studies including colorectal cancer patients and controls were conducted; the first case involving 441 patients and 658 controls, all of Ashkenazi Jewish ancestry, and the second including 199 patients and 199 matched (sex, age and ethnicity) controls. rs266729(G) showed decreased colorectal cancer risk in both studies; in the first, with an odds ratio of 0.72 (CI:0.55-0.95) and in the second, with an odds ratio of 0.52 (CI: 0.34-0.78). Combining the two studies led to an overall decreased colorectal cancer odds ratio of 0.73 (CI: 0.53-0.99) for this allele.[http://blog.23andme.com/2008/09/30/snpwatch-genetic-link-between-obesity-and-colorectal-ca...
common in clinvar
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rs63750875 is a SNP in the MSH2 gene on chromosome 2, associated with Lynch syndrome (HNPCC). The origin of this mutation appears to be in a population of Ashkenazi Jews. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 609309.0012 Characterization of chicken liver dihydrofolate reductase after purification by affinity chromatography and isoelectric focusing. Single-amplicon MSH2 A636P mutation testing in Ashkenazi Jewish patients with colorectal cancer: role in presurgical management. Homozygosity of MSH2 c.1906G-->C germline mutation is associated with childhood colon cancer, astrocytoma and signs of Neurofibromatosis type I. Classifyin...
54 snps
(hide) Conduct disorder
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[GWAS:Conduct disorder (case status)]
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[GWAS:Conduct disorder (symptom count)]
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[GWAS:Conduct disorder (case status)]
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[GWAS:Conduct disorder (case status)]
Frequency: 43.4%
References:1
References:1
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[GWAS:Conduct disorder (case status)]
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[GWAS:Conduct disorder (symptom count)]
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[GWAS:Conduct disorder (symptom count)]
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[GWAS:Conduct disorder (symptom count)]
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[GWAS:Conduct disorder (case status)]
Frequency: 57.8%
References:1
References:1
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[GWAS:Conduct disorder (case status)]
Magnitude: 0
Frequency: 77.0%
References:3
Frequency: 77.0%
References:3
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The G allele of rs10831284 is associated with a higher risk of attention deficit hyperactivity disorder (ADHD) and conduct disorder. [PharmGKB:Non-Curated GWAS results: Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (Initial Sample Size: 938 affected trios; Replication Sample Size: NR); (Region: 4q13.3; Reported Gene(s): AMOTL1, CWC15, JMJD2D; Risk Allele: rs10831284-G); (p-value= 0.000002).This variant is associated with Attention-deficit/hyperactivity disorder and conduct disorder.] [GWAS:Attention-deficit/hyperactivity disorder and conduct disorder]
14 snps
(hide) Congenital adrenal hyperplasia
miscallled by 23andMe, but should indicate being a carrier of allele for congenital adrenal hyperplasia See discussion at Congenital adrenal hyperplasia
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Congenital adrenal hyperplasia rs7769409
miscallled by 23andMe, but should indicate being a carrier of allele for congenital adrenal hyperplasia This genotype should indicate being a carrier of Congenital adrenal hyperplasia, but most 23andMe users will find this in their data due to a problem with that testing platform.
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This SNP is supposed to serve as a marker for the Q318X null allele of the 21-hydroxylase gene. This would generally be associated, when homozygous, with the most severe form of congenital adrenal hyperplasia (salt wasting). However, a random survey of 10 publicly uploaded genomes showed all 10 to be carriers. This is well out of Hardy-Weinberg equilibrium, making the accuracy of this SNP as reported by 23andme suspect. Positive results should be clinically correlated and verified in cooperation with your health care provider. [OMIM:?]
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Congenital adrenal hyperplasia rs72552754
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Congenital adrenal hyperplasia rs151344503
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Congenital adrenal hyperplasia rs72552758
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Congenital adrenal hyperplasia rs72552757
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Congenital adrenal hyperplasia rs151344506
10 snps
(hide) Coronary artery calcification
1.5x increased risk for CAD 1.5x higher risk for coronary artery disease
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rs1333049 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is most likely (C); the odds ratio associated with heterozygotes is 1.47 (CI 1.27-1.70), and for homozygotes, 1.9 (CI 1.61-2.24). This SNP has also been reported to have the highest association of any SNP studied in a subsequent experiment conducted with the resources of the German MI [Myocardial Infarction] Family Study. The initial studies were conducted on Caucasian populations. A subsequent study of Japanese and Korean patients has also found rs1333049 to be associated with increased coronary artery disease risk, with roughly similar odds ratios. '''Further reading (with comments)''' - A long-term study of a cohort of 76...
Frequency: 30.8%
References:1
References:1
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[GWAS:Coronary artery calcification]
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[GWAS:Coronary artery calcification]
Frequency: 41.6%
References:1
References:1
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[GWAS:Coronary artery calcification]
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[GWAS:Coronary artery calcification]
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[GWAS:Coronary artery calcification]
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[GWAS:Coronary artery calcification]
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[GWAS:Coronary artery calcification]
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[GWAS:Coronary artery calcification]
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[GWAS:Coronary artery calcification]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study (Initial Sample Size: 673-984 individuals, depending on measure (Framingham); Replication Sample Size: NR). This variant is associated with Coronary artery calcification.] [GWAS:Coronary artery calcification]
Frequency: 73.2%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study (Initial Sample Size: 673-984 individuals, depending on measure (Framingham); Replication Sample Size: NR). This variant is associated with Coronary artery calcification.] [GWAS:Coronary artery calcification]
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[GWAS:Coronary artery calcification]
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[GWAS:Coronary artery calcification]
14 snps
(hide) Coronary artery disease
increased risk for celiac disease increased resistance to bacterial infections
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rs3184504 is a nonsynonymous SNP in the SH2B3 gene, and it is also known as R262W. In a recent (2008) study of non-HLA SNP associations of 1600+ celiac disease patients, this SNP was considered one of the most significant. The odds ratio for the minor allele was 1.19 (CI:1.10-1.30, p=1.33x10e-7). rs653178, another SNP in strong linkage disequilibrium (r<sup>2</sup>>0.99) with rs3184504, was also associated with celiac disease. associated with type-1 diabetes 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 23andMe blog blood pressure Pharmacogenetic implications for eight common blood pressure-associated...
1.5x increased risk for CAD 1.5x higher risk for coronary artery disease
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rs1333049 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is most likely (C); the odds ratio associated with heterozygotes is 1.47 (CI 1.27-1.70), and for homozygotes, 1.9 (CI 1.61-2.24). This SNP has also been reported to have the highest association of any SNP studied in a subsequent experiment conducted with the resources of the German MI [Myocardial Infarction] Family Study. The initial studies were conducted on Caucasian populations. A subsequent study of Japanese and Korean patients has also found rs1333049 to be associated with increased coronary artery disease risk, with roughly similar odds ratios. '''Further reading (with comments)''' - A long-term study of a cohort of 76...
reduced risk of acute coronary events heterozygosity was associated with a markedly reduced risk of acute coronary events
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see also rs3732378 [OMIM:HUMAN IMMUNODEFICIENCY VIRUS TYPE 1, RAPID PROGRESSION TO AIDS]
higher risk of of coronary heart disease coronary heart disease
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rs662, also known as Q192R, is a SNP in the PON1 gene. It codes for amino acid 192 of the paraoxonase (PON) protein. Variants of this SNP affect PON catalytic efficiency and are correlated with Heart disease and trait-anxiety scores. The normal form, rs662(A), encodes a glutamine (Q), while the variant, rs662(G)), encodes an arginine (R). . While some populations show an association between this SNP and Heart disease, not all do. Perhaps the most striking finding was reported in Japanese patients with non-insulin dependent diabetes mellitus (NIDDM). NIDDM patients with either one or two rs662(G) alleles had a 9 fold higher risk of coronary heart disease compared with rs662(A;A) NIDDM patients. table of odds for cardiovascular disease outcomes 274 ovarian epithelial carcinoma cases and 452 ...
1.2x risk of coronary artery disease
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rs599839 and rs4970834 explain about 1% of the variation in circulating LDL-cholesterol levels. 'When we look at this particular genetic variance, of all the cholesterol variation among the population, 1% of it can be attributed to this particular locus,' said Sandhu. 'This is equivalent to more established genes for LDL regulation, particularly APOE.' rs646776 also linked. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins found each minor allele to increase statin effectiveness by 1.3% (rs646776, β=−0.013, s.e.=0.002, P=1.05 × 10−9 and rs12740374, β=−0.013, s.e.=0.002, P=1.05 × 10−9). 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs1746...
some risk linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil).
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
No benefit to alcohol consumption
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rs708272, also known as the TaqIB polymorphism of the CETP gene, may influence the levels of the 'good' cholesterols, the high density lipoprotein (HDL) cholesterols. Generally, the B2 allele is considered to lead to higher HDL levels. However, high HDL cholesterol, at least when combined with another HDL raising SNP (rs1800588), doesn't appear to actually protect individuals from coronary artery disease, at least based on one study of ~800 Caucasian male patients. A similarly confusing picture emerges from a study of two populations of 10,000+ individuals each. The distribution of the CETP genotype was observed to be different in population-based studies compared with studies in populations selected by high cardiovascular risk, and contradictory results were seen when trying to figure out...
1.3x increased coronary artery disease risk
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rs1333048 increases susceptibility to coronary artery disease 1.30 times for heterozygotes (AC) and 1.54 times for homozygotes (CC) rs1333048 2x risk for periodontitis and a confirmation of coronary heart disease 23andMe blog [OMIM:?]
Magnitude: 2
Frequency: 50.0%
Repute:Bad
References:77
Frequency: 50.0%
Repute:Bad
References:77
1.3x risk for Heart Attack. Normal risk for Abdominal Aortic Aneurysm and Brain Aneurysm. One copy of an SNP that increases risk of Myocardial Infarction (Heart Attack) and other Coronary Heart Disease. It has been shown that regularly eating raw vegetables and fruit can reduce the risk to the same level as people without this SNP. This SNP also has the normal medium risk of abdominal aortic aneurysm (weakened artery to abdomen and legs) or brain aneurysm (weakened artery to brain).
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This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...
increased risk for heart disease
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discussed in this blog post as possibly playing a role in coronary heart disease This SNP was also associated with increased risk for coronary artery disease in a Korean population. The association remained significant after adjusting for significant clinical covariates (P=0.001 to 0.024). We identified one risk haplotype (GGGG; P=0.017) and one protective haplotype (AAAA; P=0.007) for development of CAD. Further analysis suggested that the SNPs probably confer susceptibility to CAD in a dominance model (covariates-adjusted P=0.001 to 0.024; OR=2.37 to 1.54). Also found to be significant in a study of 416 Italian myocardial infarction patients. Found to be associated with coronary heart disease in a study of 1360 Chinese Han patients, with an odds ratio of 1.52 (CI: 1.13 - 2.04) for rs2383...
1.4x increased risk for heart disease
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rs10757274 and rs2383206 can significantly increase the risk of heart diseaseAbout one in every four Caucasians are thought to carry the variants, and their risk of coronary heart disease is increased by 30 to 40%. rs10757278] in the same region has been linked to diabetes The chromosomal region where these SNPs are located is 9p21, and has no known genes. a [http://suicyte.wordpress.com/2007/05/26/soul-searching-i/ blog post about investigating rs10757274 and rs2383206 This SNP was also associated with increased risk for coronary artery disease in a Korean population. Also found to be significant in a study of 416 Italian myocardial infarction patients. A study of 1,000+ patients with early-onset angiographic coronary artery disease (CAD) concluded that rs2383206(G) was associated with an...
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
1.9x risk 1.9x higher risk for coronary artery disease
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rs383830 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.60 (CI 1.16-2.21), and for homozygotes, 1.92 (CI 1.40-2.63).
common, but 2.2x higher risk for heart disease
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rs8055236 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.91 (CI 1.33-2.74), and for homozygotes, 2.23 (CI 1.56-3.17). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,926 cases, 2,938 controls; Replication Sample Size: (see Samani 2007); Risk Allele: rs8055236-G). This variant is associated with coronary disease.] [GWAS:Coronary disease]
Magnitude: 1.5
Frequency: 49.6%
Repute:Bad
References:3
Frequency: 49.6%
Repute:Bad
References:3
1.30x increased risk for Coronary artery disease
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rs10757272 increases susceptibility to Coronary artery disease 1.30 times for heterozygotes (CT) and 1.54 times for homozygotes (TT)
Magnitude: 1.4
Frequency: 22.3%
Repute:Good
References:4
Frequency: 22.3%
Repute:Good
References:4
Reduced risk (0.7x) for heart disease Reduced risk (0.7x) for heart disease
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rs17672135 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 0.70 (CI 0.61-0.81), and for homozygotes, 1.32 (CI 0.79-2.22). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,926 cases, 2,938 controls; Replication Sample Size: (see Samani 2007); Risk Allele: rs17672135-C). This variant is associated with coronary disease.] [GWAS:Coronary disease]
Magnitude: 1.34
Frequency: 50.0%
Repute:Bad
References:18
Frequency: 50.0%
Repute:Bad
References:18
1.34x higher risk for myocardial infarction
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rs17465637 is a SNP found to be associated with heart disease by the German MI (Myocardial infarction) Family Study group This 2011 study concluded that the only MIA3 gene SNP to be associated with increased risk for myocardial infarction is rs17465637, with an odds ratio of 1.17 (CI: 1.04-1.32) and 1.37 (CI: 1.08-1.74) for carriers of one or two (C) alleles, respectively. 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 con...
1.3x increased risk for heart disease
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rs501120 is a SNP found to be associated with heart disease in two populations by the German MI (Myocardial infarction) Family Study group. The risk allele in dbSNP orientation is rs501120(A). The odds ratio per allele is 1.33 (CI: 1.20-1.48, adjusted p=0.0248). Association of genetic variants and incident coronary heart disease in multiethnic cohorts: the PAGE study. Comparative analysis of genome-wide association studies signals for lipids, diabetes, and coronary heart disease: Cardiovascular Biomarker Genetics Collaboration. Genetic risk score and risk of myocardial infarction in Hispanics. |OA=1 }} Coronary artery disease-related genetic variant on chromosome 10q11 is associated with carotid intima-media thickness and atherosclerosis. Genetics and cardiovascular disease: Design and dev...
Some studies - but not others - report a slightly increased risk for myocardial infarction
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rs4977574 increases susceptibility to Coronary artery disease 1.30 times for heterozygotes (A;G) and 1.54 times for homozygotes (G;G) rs4977574 was found to be associated with myocardial infarction based on a study by the eMERGE network in which electronic medical records were searched to find clinical associations associated with selected SNPs. . In this study of 2,000 patients, rs4977574(G;G) homozygotes had an increased risk (odds ratio) for myocardial infarction of 1.84 (CI: 1.14−3.09, p = 0.011) [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 controls; Replication Sample Size: 9,746 cases, 9,746 controls); (Region: 9p21.3; Reported...
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[PharmGKB:Non-Curated GWAS results: Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease. (Initial Sample Size: 1,926 cases, 2,938 controls; Replication Sample Size: 7,073 cases, 7,325 controls); (Region: 6q25.3; Reported Gene(s): SLC22A3,LPAL2,LPA; Risk Allele: 4-SNP haplotype-1); (p-value= 0.000000001).This variant is associated with Coronary artery disease.] [GWAS:Coronary artery disease]
Frequency: 9.9%
References:1
References:1
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[GWAS:Coronary heart disease]
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[GWAS:None]
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15,000 individuals. Each copy of the minor T allele of SNP rs2228671 was related to a decrease of LDL-C levels by 0.19 mmol/L (95% confidence interval (CI) [0.13-0.24] mmol/L, p = 1.5x10(-10)) and a significantly lower risk of coronary artery disease (OR per copy of the T allele: 0.82, 95% CI [0.76-0.89], p = 2.1x10(-7)) [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 19p13.2; Reported Gene(s): LDLR; Risk Allele: rs2228671-G); (p-value= 0.00000000000004).This variant is associated with LDL cholesterol.] [OMIM:LOW DENSITY LIPOPROTEIN RECEPTOR; LDLR] [GWAS:Cholesterol, total]
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[GWAS:Coronary heart disease]
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[GWAS:Coronary heart disease]
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23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 Coronary Heart Disease [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 controls; Replication Sample Size: 9,746 cases, 9,746 controls); (Region: 10q11.21; Reported Gene(s): CXCL12; Risk Allele: rs1746048-C); (p-value= 0.000000007).This variant is associated with Myocardial infarction (early onset).] [GWAS:Myocardial infarction (early onset)]
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rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele in these positions increased the risk of disease (p=0.006 and, p=0.008, respectively). Carrying a haplotype with the G allele in all three promoter SNPs increased the risk of symptomatic DIP OA more than four-fold (OR 4.45, p=0.001). Carriage of the G-G diplotype indicated an increased risk of both symmetrical DIP OA (OR 1.52 95% CI 1.0...
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rs7865618 increases susceptibility to Coronary artery disease 1.23 times for heterozygotes (AG) and 1.57 times for homozygotes (AA) [GWAS:None]
Frequency: 31.9%
References:1
References:1
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rs17411031 increases susceptibility to Coronary artery disease 1.23 times for carriers of the G allele Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. Genome-wide association analyses of North American Rheumatoid Arthritis Consortium and Framingham Heart Study data utilizing genome-wide linkage results. Evaluation of genetic risk scores for lipid levels using genome-wide markers in the Framingham Heart Study. Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham heart study data. Comparative analysis of genome-wide association studies signals...
Frequency: 31.9%
References:0
References:0
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rs17489268 increases susceptibility to Coronary artery disease 1.25 times for carriers of the A allele Evaluation of genetic risk scores for lipid levels using genome-wide markers in the Framingham Heart Study. Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham heart study data.
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Coronary Heart Disease [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 controls; Replication Sample Size: 9,746 cases, 9,746 controls); (Region: 19p13.2; Reported Gene(s): LDLR; Risk Allele: rs1122608-G); (p-value= 0.000000002).This variant is associated with Myocardial infarction (early onset).] [GWAS:Coronary artery disease]
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[PharmGKB:Non-Curated GWAS results: New susceptibility locus for coronary artery disease on chromosome 3q22.3. (Initial Sample Size: 6,990 cases, 8,955 controls; Replication Sample Size: 12,417 cases, 12,411 controls); (Region: 12q24.31; Reported Gene(s): HNF1A,C12orf43; Risk Allele: rs2259816-T); (p-value= 0.0000005).This variant is associated with Coronary artery disease.] [GWAS:Coronary artery disease]
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Repeatedly associated in genome association studies with type-2 diabetes, type-1 diabetes, multiple sclerosis, and coronary artery disease, according to Risk alleles for multiple sclerosis identified by a genomewide study. An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. [GWAS:Hepatitis C induced liver cirrhosis]
1.2x risk
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rs6922269 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.17 (CI 1.04-1.32), and for homozygotes, 1.65 (CI 1.32-2.06). [PharmGKB:Non-Curated GWAS Results: Genomewide association analysis of coronary artery disease (Initial Sample Size: 1,926 cases, 2,938 controls; Replication Sample Size: 875 cases, 1,644 controls; Risk Allele: rs6922269-A).] [GWAS:Coronary disease]
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9,798 subjects show significant association between rs2548861(T) and Low serum HDL-cholesterol, a major risk factor for coronary artery disease. p = 4 x 10(-4) to 2 x 10(-5) [PharmGKB:Curated In dyslipidemic families of Mexican and European descent and in low-HDL-C cases and controls of European descent, this SNP showed significant association with low HDL-C. In two Finnish cohorts (one was prospective),the same association was significant at four time points taken over 21 years, and the T allele was the risk allele.]
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[GWAS:Coronary heart disease]
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[GWAS:Coronary artery disease]
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Coronary Heart Disease
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Coronary Heart Disease
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rs887829 is a SNP in the UGT1A1 gene. The minor allele of this SNP has been reported to be associated with higher levels of serum bilirubin, which has an inverse correlation with coronary artery disease. . This study of 2,000+ patients reports a recessive protective effect against coronary artery disease for the minor allele, with an age-adjusted odds ratio of 0.24 (CI: 0.10-0.60, p=0.0014). [PharmGKB:Curated This variant is in the promoter region of UGT1A1 and associated with serum bilirubin levels and hyperbilirubinemia in a genome wide association scan from 4300 Sardinian individuals.] [GWAS:Bilirubin levels]
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[GWAS:Coronary heart disease]
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Coronary Heart Disease [GWAS:Coronary artery disease]
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rs6475606 increases susceptibility to Coronary artery disease 1.30 times for heterozygotes (CT) and 1.54 times for homozygotes (TT) [OMIM:?]
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Coronary Heart Disease [GWAS:Coronary heart disease]
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[GWAS:Coronary artery disease]
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[GWAS:Coronary artery disease]
Frequency: 54.0%
References:4
References:4
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Coronary Heart Disease [GWAS:Coronary artery disease]
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rs7613868 increases susceptibility to Atherosclerosis 2.60 times for carriers of the T allele rs7613868 increases susceptibility to Coronary artery disease 1.80 times for carriers of the T allele
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[GWAS:Coronary heart disease]
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Coronary Heart Disease [GWAS:Serum soluble E-selectin]
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rs2230806, also known as Arg219Lys or R219K, is a SNP in the ABCA1 ATP-binding cassette, sub-family A (ABC1), member 1 gene. The rs2230806(G) allele encodes the arginine (R), and the (A) allele encodes the lysine (K). A meta-analysis published in 2011 comprising 22 studies with 6597 cases and 15,369 controls studied the association between the rs2230806 and risk for coronary artery disease. Overall, rs2230806(A) significantly associated with a higher HDL-C level in Asians and does lower the risk (odds ratio 0.76, CI: 0.68-0.85, p=3.78e-07) of coronary artery disease in Asians and Caucasians. ABCA1 modulates CSF cholesterol levels and influences the age at onset of Alzheimer's disease. Gender-specific association of ATP-binding cassette transporter 1 (ABCA1) polymorphisms with the risk of l...
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Coronary Heart Disease [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 controls; Replication Sample Size: 9,746 cases, 9,746 controls); (Region: 21q22.11; Reported Gene(s): SLC5A3, MRPS6, KCNE2; Risk Allele: rs9982601-T); (p-value= 0.00000000006).This variant is associated with Myocardial infarction (early onset).] [GWAS:Coronary artery disease]
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23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 Coronary Heart Disease [GWAS:Coronary Heart disease]
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[PharmGKB:Non-Curated GWAS results: New susceptibility locus for coronary artery disease on chromosome 3q22.3. (Initial Sample Size: 6,990 cases, 8,955 controls; Replication Sample Size: 12,417 cases, 12,411 controls); (Region: 3q22.3; Reported Gene(s): MRAS; Risk Allele: rs9818870-T); (p-value= 0.0000000000007).This variant is associated with Coronary artery disease.] [GWAS:Coronary artery disease]
The rs2243093 locus is located in the platelet glycoprotein (1bα) gene. This locus is associated with an increase risk for coronary heart disease and ischemic stroke. However, individuals who possess (T;T) are believed to be less at risk than those who possess a (C;C) genotype.
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Resides within the platelet glycoprotein (1bα) gene. The rs2243093 variant (C;C) was found to increase the odds of coronary heart disease in a clinical Chinese Han population. The (C;C) genotype is also associated with a risk of ischemic stroke. Rs2243093 is also classified in the literature as the -5T/C, Kozak sequence polymorphism. A case-control study of 246 Chinese Han patients (with preexisting coronary heart disease) reported that in comparison to the '(T;T)' genotype, the '(C;C)' genotype is associated with an increased risk for coronary heart disease with an odds ratio of 3.41 (CI: 1.19-9.75, p<0.029). A meta-analysis was performed in order to test the hypothesis that genetic variation of the platelet glycoprotein 1bα gene(which includes rs2243093 Kozak variant (n=1984...
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[GWAS:Coronary artery disease]
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[GWAS:Coronary heart disease]
Repute:Bad
References:38
References:38
~1.2x increased risk for heart disease
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rs10757274 is a SNP located in chromosomal region 9p21; to date (2009), it is the strongest genetic predictor of early myocardial infarction (heart attack) discovered so far. SNPs in this region are also associated with increased risk of stroke, abdominal aortic aneurysm (AAA), and intracranial aneurysm. Based on a large (20,000+) study primarily of Caucasian females, it appears that on its own, this single SNP does not improve on the discrimination or classification of predicted heart disease risk achieved by traditional risk factors, high-sensitivity C-reactive protein, and a family history of premature myocardial infarction. rs10757274 and rs2383206 can double the risk of heart diseaseAbout one in every four Caucasians are thought to carry the gene variants. rs10757278] in the same regi...
References:0
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rs140621530, also known as IVS3+1G>T, is a rare variant in the apolipoprotein C3 APOC3 gene. As reported in a large study published in 2014, it is one of four loss of function mutations in the APOC3 gene associated with a >40% lower average triglyceride level in individuals carrying one rs140621530(T) allele and a corresponding decrease in coronary artery disease.
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rs1800787(T;T) homozygotes are at 6 fold higher risk compared to (C;C) homozygotes or (C;T) heterozygotes for carotid atherosclerosis . This polymorphism is known as the 'C148-T' variant, and is located in at the '-148' position of the FGB gene, also known as beta fibrinogen. A meta-analysis of 7 studies did not find a significant association between the -148C/T FGB SNP and susceptibility to coronary artery disease in Chinese populations. Note: due to inconsistencies between databases and the literature, the association of this rs# with this polymorphism name as published is highly likely but not guaranteed.
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rs7802307 coronary artery disease 190 affected Asian Indian sibling pairs
normal
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rs7250581 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.06 (CI 0.79-1.43), and for homozygotes, 1.40 (CI 1.05-1.86).
normal risk
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rs1024611, also known as the -2578A>G SNP due to its position in the promoter of the monocyte chemoattractant protein-1 MCP-1 CCL2 gene, influences the production of its corresponding protein, a chemokine involved in inflammatory responses. In a study focusing on 679 apparently healthy siblings of people with premature heart disease, investigators found that carriers of an rs1024611(C) allele - oriented as in dbSNP, not as published - independently predicted the risk of exercise induced ischemia in general. The odds ratio was reported to be 1.86 (CI: 1.14-3.04, p=0.014), regardless of race, age, sex and other factors. However, it is not clear if this risk carries over to individuals who lack siblings with heart disease. discussed in the 23andMe blog as being relevant to HIV rs1024611 is...
normal
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rs688034 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.11 (CI 0.98-1.25), and for homozygotes, 1.62 (CI 1.34-1.95). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,926 cases, 2,938 controls; Replication Sample Size: (see Samani 2007); Risk Allele: rs688034-T). This variant is associated with coronary disease.] [GWAS:Coronary disease]
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
common in complete genomics
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rs1800588, also known as the -514C/T polymorphism of the LIPC gene, may influence the levels of the 'good' cholestorols, the high density lipoprotein (HDL) cholesterols. Generally, the (T) allele (as published) is considered to lead to higher HDL levels. However, high HDL cholesterol, at least when combined with another HDL raising SNP (rs708272), doesn't appear to actually protect individuals from coronary artery disease, at least based on one study of ~800 Caucasian male patients. Associations between HDL-cholesterol and polymorphisms in hepatic lipase and lipoprotein lipase genes are modified by dietary fat intake in African American and White adults. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. Low-density lipoprotein and high-density lipopr...
common on affy axiom data
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rs3732378 VAL249ILE is tightly linked to neighboring rs3732379 THR280MET The protein receptor with both variant amino acids is known as CX3CR1-M280. the minor alleles of this pair are associated with *more rapid progression to full-blown AIDS and probably increased susceptibility to HIV infection *reduced risk of acute coronary events *increased risk of age related macular degeneration [OMIM:?]
Magnitude: 0
Frequency: 69.0%
References:14
Frequency: 69.0%
References:14
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23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 Genetic susceptibility to coronary heart disease in type 2 diabetes: 3 independent studies. Genetics of diabetes complications. Using a latent growth curve model for an integrative assessment of the effects of genetic and environmental factors on multiple phenotypes. Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoids: a genome-wide association study. Genetics of coronary artery disease: focus on genome-wide association studies. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to...
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23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 Coronary Heart Disease [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 controls; Replication Sample Size: 9,746 cases, 9,746 controls); (Region: 2q33.1; Reported Gene(s): WDR12; Risk Allele: rs6725887-C); (p-value= 0.00000001).This variant is associated with Myocardial infarction (early onset).] [GWAS:Myocardial infarction (early onset)]
Magnitude: 0
Frequency: 76.1%
Repute:Good
References:8
Frequency: 76.1%
Repute:Good
References:8
normal
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This position is odd. Under the older reference genome build36, it was on the plus strand; in build37 it is on the minus strand. This makes it very prone to some ambiguous flip confusion in the literature, plus, 23andMe users have self-reported the flipped form. IN addition, instead of the usual SNP listed as having 2 alleles, all 4 alleles are reported in dbSNP, even if this is probably due to the strand changes. dbSNP currently says the normal allele is C, and T is the rare geno which causes a premature stop, early in the gene. We at SNPedia suspect that the A & G alleles are not common enough to have ever been genuinely reported, but for de-novo mutations each allele would be non-synonymous and result in a different amino acid. http://snpedia.blogspot.com/2012/12/snpedias-nightmare-befo...
Magnitude: 0
Frequency: 85.8%
References:4
Frequency: 85.8%
References:4
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Based on a large study (~6,000 cases and 14,000 controls) of both European and Japanese populations, the rs12413409(G) allele has been associated with higher risk of aneurysm, with an odds ratio per allele of 1.29 (CI:1.19-1.40, p=1.2e-09). Also: 23andMe blog blood pressure Coronary Heart Disease High Blood Pressure (Hypertension) [OMIM:?] [GWAS:None]
Magnitude: 0
Frequency: 86.2%
Repute:Good
References:22
Frequency: 86.2%
Repute:Good
References:22
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rs10455872, was associated with about 1.5-fold increased risk of Coronary Heart Disease. celera Genetic variation in LPAL2, LPA, and PLG predicts plasma lipoprotein(a) level and carotid artery disease risk. Lipoprotein(a) genetic variants associated with coronary and peripheral vascular disease but not with stroke risk in the Heart Protection Study. Single-nucleotide polymorphisms in LPA explain most of the ancestry-specific variation in Lp(a) levels in African Americans. Variation in LPA is associated with Lp(a) levels in three populations from the Third National Health and Nutrition Examination Survey. Cost-effectiveness model of use of genetic testing as an aid in assessing the likely benefit of aspirin therapy for primary prevention of cardiovascular disease. [OMIM:?] [GWAS:None]
normal
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The INSR A-603G promoter rs1864010 SNP, which is located within a known Sp1-binding site, was associated with the risk of colorectal cancer, with carriers of the G allele having a decreased risk (odds ratios (OR) 0.71, 95% confidence interval (CI) 0.54-0.93). Carrying the variant allele of the IRS1 Gly972Arg rs1801278 SNP further decreased the risk among the INSR-603G allele carriers (OR 0.28, 95% CI 0.11-0.70) multiple myeloma *rs1801278 [C/T versus C/C genotypes; OR, 4.3; 95% confidence interval (CI), 1.5-12.1] *rs6684439 (T/T versus C/C; OR, 2.9; 95% CI, 1.2-7.0) *rs7529229 (C/C versus T/T; OR, 2.5; 95% CI, 1.1-6.0) *rs8192284 (C/C versus A/A; OR, 2.5, 95% CI, 1.1-6.0)
common in complete genomics
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rs2066992 coronary artery disease 190 affected Asian Indian sibling pairs
common in complete genomics
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23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 Coronary Heart Disease [GWAS:Hematological and biochemical traits]
normal
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rs3798220, also known as I4399M or Ile4399Met, is a SNP in the apolipoprotein(A) LPA gene that has been reported to be associated with elevated plasma lipoprotein(a) [Lp(a)] and increased cardiovascular risk, and in particular, coronary artery disease. In one study, 25,131 initially healthy Caucasian participants in the Women's Health Study were followed for ~10 years. rs3798220(C) allele carriers (3.7%) in the placebo (i.e. not receiving aspirin) group had a 2x higher risk of major cardiovascular events than non-carriers (age-adjusted hazard ratio (HR) of 2.21, CI: 1.39-3.52). Among rs3798220(C) carriers, the risk was reduced more than twofold by aspirin: for aspirin compared with placebo the age-adjusted HR was 0.44 (CI: 0.20-0.94). The risk was not significantly reduced among non-carrie...
Magnitude: 0
Repute:good
References:2
Repute:good
References:2
common in ClinVar
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rs138326449, also known as IVS2+1G>A, is a rare variant in the apolipoprotein C3 APOC3 gene. As reported in two large studies published in 2014, rs138326449 is one of several loss of function mutations in the APOC3 gene associated with a >40% lower average triglyceride level in individuals carrying one rs138326449(A) allele and a corresponding decrease in coronary artery disease.
common in complete genomics appears to be common on the 23andMe platform
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rs1800796 IL-6 572G>C polymorphism (and h.211 haplotype) is associated with abdominal aortic aneurysm (AAA). The risk allele is C. Our results provide evidence that there is a clear genetic influence of IL6 -572C>G polymorphism on plasma levels of fibrinogen and CRP, but this polymorphism does not lead to elevated blood pressure. rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele ...
79 snps
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normal
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Something seems wrong between dbSNP and the results from 23andMe and FTDNA. See Talk:Rs4148323 for more information. rs4148323, a SNP also known as 211G>A or G71R, occurs in the UGT1A1 gene, and defines the UGT1A1*6 allele. This allele is associated with Gilbert's syndrome among Asians, Crigler-Najjar syndrome type II (CN-II), and transient familial neonatal hyperbilirubinemia. rs4148323(A) in exon 1 of the UGT1A1 gene is associated with hyperbilirubinemia. rs4148323 and several other nearby SNPs help predict serum total bilirubin levels, based on a study of 750 Japanese. [PharmGKB:Curated *6 is the most common UGT1A1 coding variant found in Asians. It may result in reduced capacity to metabolize irinotecan and hence irinotecan toxicity.] [OMIM:UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEP...
2 snps
(hide) Crohn's disease
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DeCode reports that rs2301436 is associated with susceptibility to Crohn's disease. [PharmGKB:Non-Curated GWAS Results: Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease (Initial Sample Size: 3,230 cases 4,829 controls; Replication Sample Size: 2,325 cases 1,809 controls 1,339 affected trios; Risk Allele: rs2301436-T).] [GWAS:Crohn's disease] [GWAS:Crohn's disease]
60% reduction in HIV viral load The rs9264942(C;T) genotype is reported to be associated with a 60% reduction in viral load in HIV-infected individuals. See also rs9264942 and HIV.
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This SNP (C/T) is in 5' region of the HLA-C gene, 35 kb away from transcription initiation in or around the HLA-C gene. 'People with this tiny sequence variation, dubbed rs9264942, appear to have up to 90% less virus in their systems than those who carry other polymorphisms. About 10% of Europeans appear to carry two copies of rs9264942, which leads to an average 90% viral load reduction. About 50% of Europeans carry one copy, which gives a 60% reduction. By comparison, less than 40% of people of African descent appear to carry a single copy of the polymorphism.' Genetic variation may lower HIV load by 90% They are referring to the (C;C) genotype giving a 90% reduction and the (C;T) giving a 60% reduction. dbSNP page This SNP is also reported to account for 6.5% of the 15% variation in vir...
Magnitude: 2
Frequency: 0.0%
Repute:Bad
References:2
Frequency: 0.0%
Repute:Bad
References:2
Increased risk for Crohn's Disease
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease]
1.5x increased risk for Crohn's disease; 2x increased risk for Graves' disease
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SNP rs2201841, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. Another study found that the 'A allele' and 'AA genotype' were significantly overrepresented in Graves' disease patients with Graves ophthalmopathy, based on 216 North American patients. The odds ratios reported were 2.04 for the allele (p=1x10<sup>-4</sup>), and for the so-called 'AA' genotype (presumably rs2201841(T;T) when correctly oriented to the dbSNP orientation), 2.4 (p=1x10<sup>-4</sup>). 23andMe blog psoriasis Europeans *rs2201841(G) 1.13x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication S...
Magnitude: 2
Frequency: 38.9%
Repute:Bad
References:40
Frequency: 38.9%
Repute:Bad
References:40
1.5x increased risk for certain autoimmune diseases; 2x increased risk for Graves disease
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SNP rs10889677, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele for this SNP has been associated with increased risk for ankylosing spondylitis in a large study of over 1,000 Caucasian patients. The odds ratio is 1.3 (p=1.3x10e-6). In a study of 216 North American patients with Graves' disease, the C allele of rs10889677 was 2.03x overrepresented (p=1.3x10<sup>–4</sup>), and the homozygous rs10889677(C;C) genotype was also overrepresented (2.36x; p=1.4x10<sup>-4</sup>) in Graves ophthalmopathy patients. A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ance...
1.3x risk for Crohn's disease
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rs7807268 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.38 (CI 1.20-1.60), and for homozygotes, 1.47 (CI 1.24-1.74). * Note: there is a slight amount of ambiguity over the orientation of this SNP information relative to the dbSNP entry.
1.9x higher risk for Crohn's disease
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rs17221417 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.29 (CI 1.13-1.46), and for homozygotes, 1.92 (CI 1.58-2.34). Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Individual disease risk and multimetric analysis of Crohn disease. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. [OMIM:NUCLEOTIDE-BINDING OLIGOMERIZATION DOMAIN PROTEIN 2; NOD2]
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
Normal risk of Atopic Dermatitis.
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23andMe blog associated rs7927894(T) with Crohn’s disease 1.16x and atopic dermatitis [PharmGKB:Non-Curated GWAS results: A common variant on chromosome 11q13 is associated with Dermatitis, Atopic. (Initial Sample Size: 939 cases, 975 controls, 1,097 family members; Replication Sample Size: 2,637 cases, 3,957 controls); (Region: 11q13.5; Reported Gene(s): C11orf30; Risk Allele: rs7927894-A); (p-value= 0.0000000008).This variant is associated with Dermatitis, Atopic.] [OMIM:?] [GWAS:Atopic dermatitis]
1.63x increased risk of developing Crohn's disease
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rs6908425 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.63 (CI 1.38-2.25), and for homozygotes, 1.95 (CI 1.43-2.67). [OMIM:?] [GWAS:Crohn's disease]
1.3x increased risk for Crohn's disease with ileal involvement
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rs3814570 is a SNP in the transcription factor 7-like 2 (T-cell specific, HMG-box) TCF7L2 gene. A study of 784 Crohn's disease patients with ileal involvement concluded that rs3814570 was associated with increased risk, but not with risk for colonic Crohn's disease or ulcerative colitis. The odds ratio was 1.27 (CI: 1.07 - 1.52, p = 0.00737). Evidence for association between polycystic ovary syndrome (PCOS) and TCF7L2 and glucose intolerance in women with PCOS and TCF7L2.
1.16x increased risk of developing Crohn's disease
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rs6601764 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.16 (CI 1.01-1.33), and for homozygotes, 1.52 (CI 1.28-1.80).
1.4x increased risk for Crohn's disease in Caucasians
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rs2241880, a SNP in the ATG16L1 gene encoding a threonine to alanine substitution ('T300A') in a protein known to be involved in the function of the epithelial cells lining the intestine, has been associated with Crohn's disease in several recent studies. In another recent (2007) report, rs2241880 is confirmed to be associated with both Crohn's disease and ileal disease, but additionally, the authors calculate risk for individuals who are homozygotes for this SNP plus 2 others (in the IBD5 and NOD2 genes). Individuals homozygous for the risk alleles for all 3 of these SNPs are estimated to be at 20 fold higher risk (CI ~9-49) for Crohn's disease. From the largest most recent survey, the Crohn's disease-associated SNPs for IBD5 and NOD2 are, respectively, rs6596075 and rs17221417. associate...
1.1x risk Crohn's Disease
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rs9858542 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.09 (CI 0.96-1.24), and for homozygotes, 1.84 (CI 1.49-2.26). [PharmGKB:Non-Curated GWAS results: Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: 1,182 cases, 2,024 controls). This variant is associated with Crohn's disease.] [OMIM:INFLAMMATORY BOWEL DISEASE 12; IBD12] [GWAS:Ulcerative colitis] [GWAS:Crohn's disease]
Magnitude: 1.1
Frequency: 91.8%
Repute:Bad
References:100
Frequency: 91.8%
Repute:Bad
References:100
Normal, but higher risk for certain autoimmune diseases. Almost everyone has this form, but it indicates a slightly higher risk of Ankylosing Spondylitis, Crohn's Disease (1.09x), Psoriasis (1.06x), and Ulcerative Colitis (1.06x). The risk is much greater than for the rare version. This is the interleukin-23 (IL-23) receptor. Media:http://www.the-rheumatologist.org/details/article/2528901/Neutralizing_IL-23_and_Its_Targets_May_Improve_Ankylosing_Spondylitis.html] Neutralizing IL-23 and Its Targets May Improve Ankylosing Spondylitis by Lara C. Pullen, PhD in The Rheumatologist newsmagazine ]
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A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-1....
Frequency: 2.7%
References:1
References:1
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[GWAS:Crohn's disease]
Frequency: 7.1%
References:0
References:0
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rs10512734 increases susceptibility to Crohn's disease 1.63 times for carriers of the A allele
1.7x increased risk for Crohn's disease
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rs2076756 is a SNP of the NOD2 gene found in a genome-wide association study to be associated with Crohn's disease. In several European populations, the minor NOD2 allele, rs2076756(G), is associated with increased risk for Crohn's disease. The odds ratio (pooled over several populations) is 1.71 (CI: 1.42-2.05, p=6x10<sup>-8</sup>). Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. Strategies and issues in the detection of pathway enrichment in genome-wide association studies. Detecting gene-gene interactions that underlie human diseases. Role of NOD1/CARD4 and NOD2/CARD15 gene polymorphisms in cancer etiology. [PharmGKB:C...
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rs9292777 is in linkage disequilibrium with a polymorphism that increases susceptibility to Crohn's disease 1.46 times for carriers of the T allele [GWAS:Crohn's disease]
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rs1373692 increases susceptibility to Crohn's disease 1.46 times for carriers of the G allele [PharmGKB:Non-Curated GWAS results: Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4 (Initial Sample Size: 547 cases, 928 controls; Replication Sample Size: 1,266 cases, 559 controls, 428 trios). This variant is associated with Crohn's disease.] [OMIM:INFLAMMATORY BOWEL DISEASE 18; IBD18] [GWAS:Crohn's disease]
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rs348594 is in linkage disequilibrium with a polymorphism that increases susceptibility to Crohn's disease 1.36 times for carriers of the A allele
0.72x decreased risk for Crohn's disease
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rs1992660 is a SNP upstream of the PTGER4 gene that was found in a genome-wide association study to be associated with Crohn's disease. In several European populations, the most common allele, rs1992660(A), was associated with increased risk for Crohn's disease. Conversely, the odds ratio (pooled over several populations) for the minor allele, rs1992660(G), was 0.72 (CI: 0.60-0.86, p=0.0005). [PharmGKB:Non-Curated GWAS results: Systematic association mapping identifies NELL1 as a novel IBD disease gene (Initial Sample Size: 393 cases, 399 controls; Replication Sample Size: 2,920 cases, 1,961 controls, 1,248 trios). This variant is associated with Irritable bowel syndrome.] [OMIM:INFLAMMATORY BOWEL DISEASE 18; IBD18] [GWAS:Irritable bowel syndrome]
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DeCode reports that rs1551398 is associated with susceptibility to Crohn's disease. [GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
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DeCode reports that rs762421 is associated with susceptibility to Crohn's disease. Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [GWAS:Crohn's disease]
increased risk for hypertension
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rs5051 is a SNP in the promoter of the angiotensin AGT gene, and presumably due to it's tight linkage with rs699, the rs5051(T) allele - as oriented to the dbSNP entry, not as published - has been associated with increased risk for hypertension and complications thereof. rs699(T) is associated with higher plasma angiotensinogen levels, and therefore the increased risk of essential hypertension. The frequency of the rs699(T) allele is also generally higher in African populations compared to Caucasian populations, correlating to the higher incidence of hypertension in African population. rs5051 is also known as 'A-6G'. For more details, see rs699. rs5051(T;T) homozygotes have been reported to be at increased risk for Crohn's disease, as based on one cohort of ~350 Australian patients. The od...
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A Danish case-control study comprising 373 Crohn's disease and 541 ulcerative colitis patients (and 796 healthy controls) concluded that carriers of the homozygous COX-2 and MDR1 intron 3 variant (rs3789243) had a relatively high risk of CD, odds ratio (95% CI) (OR (95% CI))=2.86 ((1.34-5.88) p=0.006) and 1.39 ((0.99-1.92) p=0.054), respectively, and for UC of 2.63 ((1.33-5.26) p=0.005) and 1.28 ((0.96-1.51) p=0.093), respectively, assuming complete dominance. [PharmGKB:Curated This variant maybe associated with drug resistance in chinese epilepsy patients. Sample size: 464 chinese epilepsy patients (270 drug responsive, 194 drug resistant).] [OMIM:ATP-BINDING CASSETTE, SUBFAMILY B, MEMBER 1; ABCB1]
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Genetic analysis of innate immunity in Crohn's disease and ulcerative colitis identifies two susceptibility loci harboring CARD9 and IL18RAP. Elucidating the chromosome 9 association with AS; CARD9 is a candidate gene. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [GWAS:Ulcerative colitis]
Frequency: 26.5%
References:1
References:1
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Also known as IBD5-IGR2230, the G>A mutation is associated with an increased risk of Crohn's Disease. MAST3: a novel IBD risk factor that modulates TLR4 signaling.
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[GWAS:Crohn's disease]
Frequency: 29.2%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease]
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Mapping the genetic architecture of gene expression in human liver. Association of MHC SNP genotype with susceptibility to type 1 diabetes: a modified survival approach. A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Quantitative trait loci for CD4:CD8 lymphocyte ratio are associated with risk of type 1 diabetes and HIV-1 immune control. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. D...
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Strategies and issues in the detection of pathway enrichment in genome-wide association studies. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. Association of novel genetic Loci with circulating fibrinogen levels: a genome-wide association study in 6 population-based cohorts. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [OMIM:INFLAMMATORY BOWEL DISEASE 5; [[IBD5]]] [GWAS:Crohn's disease]
Frequency: 31.2%
References:7
References:7
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Refined genomic localization and ethnic differences observed for the IBD5 association with Crohn's disease. Analysis of candidate genes on chromosomes 5q and 19p in celiac disease. IGR2096a_1 T and IGR2198a_1 C alleles on IBD5 locus of chromosome 5q31 region confer risk for Crohn's disease in Hungarian patients. Interaction of the major inflammatory bowel disease susceptibility alleles in Crohn's disease patients. [OMIM:INFLAMMATORY BOWEL DISEASE 5; [[IBD5]]] [GWAS:None]
Magnitude: 1
Frequency: 31.9%
Repute:Good
References:8
Frequency: 31.9%
Repute:Good
References:8
Normal risk of developing Crohn's disease
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rs10883365 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.2 (CI 1.03-1.39), and for homozygotes, 1.62 (CI 1.37-1.92). The association between rs10883365 and Crohn's disease was replicated in a Japanese population. Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease. Worldwide population differentiation at disease-associated SNPs. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. Unbiased estimation of odds ra...
Frequency: 31.9%
References:5
References:5
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[OMIM:INFLAMMATORY BOWEL DISEASE 20; IBD20] [GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
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rs8050910 increases susceptibility to Crohn's disease 1.19 times for carriers of the T allele [OMIM:INFLAMMATORY BOWEL DISEASE 1; IBD1]
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Crohn's disease and sarcoidosis 1,317 patients (660 CD and 657 SA) and 1,091 controls. rs1398024(A) odds ratio of 0.81 (95% confidence interval [CI], 0.69-0.96) [PharmGKB:Non-Curated GWAS Results: Genome-wide association study anaylsis in sarcoidosis and Crohn disease unravels a common susceptibility locus on 10p12.2 (Initial Sample Size: 382 CD cases, 398 SA cases, 394 controls; Replication Sample Size: 660 CD cases, 657 SA cases, 1,091 controls; Risk Allele: rs1398024-A). This variant is associated with Sarcoidosis and Crohn disease.] [GWAS:Crohn's disease and Sarcoidosis (combined)]
?
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rs1793004 is a SNP in the NELL1 gene that was found in a genome-wide association study to be associated with Crohn's disease. In several European populations, the most common allele, rs1793004(C), was associated with increased risk for Crohn's disease. Conversely, the odds ratio (pooled over several populations) for the minor allele, rs1793004(G), was 0.89 (CI: 0.69-1.14, p=0.0037). [PharmGKB:Non-Curated GWAS results: Systematic association mapping identifies NELL1 as a novel IBD disease gene (Initial Sample Size: 393 cases, 399 controls; Replication Sample Size: 2,920 cases, 1,961 controls, 1,248 trios). This variant is associated with Irritable bowel syndrome.] [GWAS:Irritable bowel syndrome]
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rs2305767 (P = 1.16 x 10(-4); OR 1.41, 95% CI 1.18-1.67). We demonstrate significant association of allelic variants in MYO9B with schizophrenia Crohn's disease rs2305767 associated with inflammatory bowel disease (IBD) overall (corrected P-value 0.002, odds ratio [OR] 0.76, 95% confidence interval [CI] 0.67-0.86)
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[PharmGKB:Non-Curated GWAS Results: Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease (Initial Sample Size: 3,230 cases 4,829 controls; Replication Sample Size: 2,325 cases 1,809 controls 1,339 affected trios; Risk Allele: rs744166-A).] [OMIM:INFLAMMATORY BOWEL DISEASE 22; IBD22] [GWAS:Crohn's disease]
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Associated with at least one 'mortality outcome' in a study of ~10,000 individuals. Separately, a meta-analysis of 10 case-control studies, including over 2,200 Graves' disease cases, concluded that rs1799964(C) carriers were associated with the disease. [PharmGKB:Curated Haplotype tagging SNP.] [GWAS:Crohn's disease]
Frequency: 38.1%
References:7
References:7
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DeCode reports that rs10045431 affects susceptibility to Crohn's disease. Sequence variants in the genes for the interleukin-23 receptor (IL23R) and its ligand (IL12B) confer protection against psoriasis. Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease. Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication i...
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Heterozygotes for SNP rs11362, located in the DEFB1 gene, are reported to be at increased risk for colonic Crohn's disease - but not the ileal or ileocolonic forms of the disease - based on a study of 190 Caucasians. The odds ratio is 2.393 (CI: 1.18-4.87, p=0.02). G-20A rs11362(A;G) 2.4x risk colonic and ileocolonic Crohn's disease but no association was detected for the ileal localization
Frequency: 38.9%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease]
Frequency: 38.9%
Repute:Bad
References:11
Repute:Bad
References:11
1.4x risk
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rs11805303 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.39 (CI 1.22-1.58), and for homozygotes, 1.86 (CI 1.54-2.24). [OMIM:INTERLEUKIN 23 RECEPTOR; IL23R]
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rs2631372 increases susceptibility to Crohn's disease 1.28 times for carriers of the C allele
Frequency: 39.8%
References:6
References:6
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[GWAS:Crohn's disease]
Magnitude: 1
Frequency: 39.8%
Repute:Good
References:0
Frequency: 39.8%
Repute:Good
References:0
Normal risk of developing Crohn's disease
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rs12037606 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.22 (CI 1.07-1.40), and for homozygotes, 1.52 (CI 1.28-1.82).
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[GWAS:Inflammatory bowel disease]
1.5x risk
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SNP rs1004819, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele is also reported to increase the risk for developing ankylosing spondylitis, based on a large study of over 1,000 Caucasian patients. The odds ratio is 1.2 (p=8.8x10e-5). significant associations with rs1004819, rs7517847, and rs11209026. Having any CARD15 variant was associated with a significant risk for CD (P < 0.0001). Investigation of the IL23R gene in a Spanish rheumatoid arthritis cohort. rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and OCTN1/2 variants. CARD15 and IL23R influences Crohn's disease susceptibility but not disease phenotype in a Brazili...
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DeCode reports that rs1456893 is associated with susceptibility to Crohn's disease. [GWAS:Crohn's disease]
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[GWAS:Inflammatory bowel disease]
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[GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
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via spitoon reports about which identifies 32 snps relevant to Crohn's disease: '''Out of a possible total of 46, 80% of people will have between 17 and 25 copies of the riskier versions of these SNPs. Because there are so many of these SNPs--and because the riskier versions are often more common than their less risky counterparts--even people at the high end of the distribution are not much more likely than average to develop Crohn's disease.''' *rs3197999 A 1.2 *rs2188962 T 1.25 *rs2476601 G 1.31 *rs2274910 C 1.14 *rs9286879 G 1.19 *rs10045431 C 1.11 *rs6908425 C 1.21 *rs2301436 T 1.21 *rs1456893 A 1.2 *rs1551398 A 1.08 *rs10758669 C 1.12 *rs3764147 G 1.25 *rs2872507 A 1.12 *rs744166 A 1.18 *rs762421 G 1.13 *rs3763313 C 1.19 Proxy snps on 23andMe *rs7714584 G 1.33 *rs6478108 T 1.22 *rs12...
Frequency: 44.2%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease]
Frequency: 44.2%
References:6
References:6
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[OMIM:INFLAMMATORY BOWEL DISEASE 23; IBD23] [GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease]
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found no association with Crohn's disease for rs1799946, but did find associations for two other DEFB1 SNPs, rs11362 and rs1800972.
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[PharmGKB:Non-Curated GWAS Results: Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes (Initial Sample Size: 4,549 cases, 5,579 controls; Replication Sample Size: 24,194 cases, 55,598 controls; Risk Allele: rs864745-T).] [GWAS:Crohn's disease] [GWAS:Type 2 diabetes]
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DeCode reports that rs7746082 is associated with susceptibility to Crohn's disease. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [PharmGKB:Non-Curated GWAS Results: Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease (Initial Sample Size: 3,230 cases 4,829 controls; Replication Sample Size: 2,325 cases 1,809 controls 1,339 affected trios; Risk Allele: rs7746082-C).] [GWAS:Crohn's disease]
possibly reduced risk for Crohn's disease
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the association may be specific to Crohn's disease, as opposed to all types of IBD. significant associations with rs1004819, rs7517847, and rs11209026. Having any CARD15 variant was associated with a significant risk for Crohn's disease (P < 0.0001). rs7517847 (P=4.9x10(-9), OR 0.65, 0.56-0.75), is statistically independent of rs11209026. Replicated reduced risk for Crohn's disease with the rs7517847(G) allele in a study of Italian patients, but not ulcerative colitis. Each incidence of the G allele was associated with a decrease in Crohn's Disease in New Zealand populations studied. Investigation of the IL23R gene in a Spanish rheumatoid arthritis cohort. rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and O...
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[GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
Frequency: 46.2%
References:2
References:2
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Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [OMIM:?] [GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
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DeCode reports that rs1736148 is associated with susceptibility to Crohn's disease.
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[OMIM:INFLAMMATORY BOWEL DISEASE 16; IBD16] [GWAS:Crohn's disease]
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Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [GWAS:Crohn's disease]
Frequency: 48.7%
References:1
References:1
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[GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
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A study of 507 CD patients, 475 UC patients and 576 controls from New Zealand Caucasians found that rs4821544, a SNP in the NCF4 gene, was associated specifically with ileal Crohn's disease but not with other forms of inflammatory bowel disease. The reported odds ratio was 1.425, CI: 1.092-1.859, p=0.009. rs4821544 increases susceptibility to Crohn's disease 1.19 times for carriers of the C allele [OMIM:INFLAMMATORY BOWEL DISEASE 1; IBD1] [GWAS:None]
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Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [GWAS:Crohn's disease]
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Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. Assessing the reproducibility of asthma candidate gene associations, using genome-wide data. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [OMIM:INFLAMMATORY BOWEL DISEASE 22; IBD22] [GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
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Associated with increased risk for Crohn's disease in a study of 380 Korean patients. This SNP is associated with greater susceptibility to leprosy in Asians, according to the 23andMe blog. The risk allele is T, and the odds ratio is 1.37. The TNFSF15 gene encodes a cytokine protein in the tumor necrosis factor (TNF) family. TNFSF15 is an ethnic-specific IBD gene. Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. TNFSF15 polymorphisms are associated with susceptibility to inflammatory bowel disease in a new European cohort. IBD-associated TL1A gene (TNFSF15) haplotypes determine increased expression of TL1A protein. Comprehensive linkage and association analyses identify haplotype, near to the TNFSF15 gene, significantly associated with spondyloarthrit...
Frequency: 50.8%
References:5
References:5
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[OMIM:INFLAMMATORY BOWEL DISEASE 15; IBD15] [GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
Frequency: 51.8%
References:14
References:14
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[GWAS:Crohn's disease]
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[GWAS:None]
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rs2066843 increases susceptibility to Crohn's disease 4.09 times for carriers of the T allele [PharmGKB:Curated rs2066843 was found to be associated with Crohn's disease in GWAS of a European, non-Jewish case-control cohort.]
Frequency: 54.0%
Repute:Bad
References:6
Repute:Bad
References:6
1.2x risk
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rs10210302 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.19 (CI 1.01-1.41), and for homozygotes, 1.85 (CI 1.56-2.21). [OMIM:INFLAMMATORY BOWEL DISEASE 10; IBD10]
1.2x risk
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rs7753394 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.21 (CI 1.04-1.40), and for homozygotes, 1.48 (CI 1.25-1.76).
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Variant in the NOD2 gene associated with greater susceptibility to leprosy in Asians, according to the 23andMe blog. The risk allele is C, and the odds ratio is 1.59. Another gene associated with susceptibility to leprosy is TNFSF15. SNPs in both the NOD2 and TNFSF15 genes are also associated with susceptibility to Crohn's disease. Leprosy Susceptibility [GWAS:Leprosy]
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[GWAS:None]
0.77x risk for Crohn's disease
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The less common allele of rs1128535, a SNP in the TRAIP gene, may have a protective effect against the development of Crohn's disease, based on a study of 469 Caucasian patients. The reported odds ratio is 0.77 (CI: 0.67-0.89, p=0.002). Note that rs1128535 is highly correlated (r<sup>2</sup> > 0.8) to nonsynonymous SNPs in the nearby MST1R gene, rs2230590 and rs1062633, also known as Arg523Gln and Gly1335Arg, respectively.
Frequency: 57.5%
Repute:Bad
References:11
Repute:Bad
References:11
1.2x risk
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rs10761659 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.23 (CI 1.05-1.45), and for homozygotes, 1.55 (CI 1.3-1.84). [OMIM:INFLAMMATORY BOWEL DISEASE 15; IBD15] [GWAS:None]
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[GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
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Variant in the C13orf31 region associated with increased susceptibility to leprosy, according to the 23andMe blog 23andMe blog. The risk allele is G, and the odds ratio is 1.68. Other genes associated with both Crohn's disease and leprosy include NOD2 and TNFSF15, according to 23andMe's blog. Leprosy Susceptibility [PharmGKB:Non-Curated GWAS Results: Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease (Initial Sample Size: 3,230 cases 4,829 controls; Replication Sample Size: 2,325 cases 1,809 controls 1,339 affected trios; Risk Allele: rs3764147-G).] [OMIM:?] [GWAS:Leprosy] [GWAS:Crohn's disease]
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[GWAS:Crohn's disease]
normal risk of rheumatoid arthritis, SLE, Sjögren's syndrome, type-1 diabetes, and primary biliary cirrhosis.
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune dise...
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DeCode reports that rs9286879 is associated with susceptibility to Crohn's disease. [OMIM:GERODERMA OSTEODYSPLASTICUM; GO] [GWAS:Crohn's disease]
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rs4613763 increases susceptibility to Crohn's disease 1.56 times for carriers of the C allele [OMIM:INFLAMMATORY BOWEL DISEASE 18; IBD18] [GWAS:Crohn's disease]
Frequency: 71.7%
References:1
References:1
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[GWAS:Crohn's disease]
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Carriers of the C allele of rs224136 reportedly have 1.67 times higher susceptibility to Crohn's disease. Rs224136 is not a major genetic risk factor for susceptibility to Crohn's disease in the German population. [PharmGKB:Non-Curated GWAS results: Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis (Initial Sample Size: 946 cases, 977 controls; Replication Sample Size: 530 trios, 353 cases, 207 controls). This variant is associated with Crohn's disease.] [OMIM:INFLAMMATORY BOWEL DISEASE 1; IBD1] [GWAS:Crohn's disease]
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[GWAS:None]
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[GWAS:Crohn's disease]
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linked to Crohn's disease and type-1 diabetes Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants. Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1). The expanding genetic overlap between multiple sclerosis and type I diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1. Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cyto...
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease]
References:1
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[GWAS:Crohn's disease]
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rs1800471 encodes a change at codon 25 of the TGFB1 gene. It is reported to predispose several organs to fibrosis, and in relation to Crohn's disease, it was associated with stricturing Crohn's disease (odds ratio 2.63, CI: 1.16-5.88, p=0.01) and a shorter time to intestinal resection (p = 0.06) in a study of several hundred Australian patients. [PharmGKB:Curated In conjunction with polymorphism at codon 10, this SNP defines high-, medium- or low-producer haplotype. The Arg allele is associated with higher blood pressure. The C allele is associated with susceptibility to EBV-associated post-transplant lymphoproliferative disorder. The C allele is associated with susceptibility to chronic periodontitis; The G allele may be associated with brucellosis susceptibility. This SNP may play a rol...
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[GWAS:None]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease]
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rs11739135 is reported to confer susceptibility to Crohn's disease.
1.4x increased risk of psoriasis, psoriatic arthritis
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IL12B gene SNP, part of a haplotype with rs3212227 associated with psoriasis. rs6887695 confirmed to be associated with psoriasis in another study A study of 500+ patients with psoriatic arthritis (PsA) concluded that the odds ratio for rs6887695(G;G) carriers was 1.43 (CI: 1.18-1.74). The effect sizes observed in patients with PsA appear to be smaller than those previously reported in patients with psoriasis, suggesting that both loci are primarily associated with psoriasis susceptibility rather than primarily with psoriatic arthritis. [OMIM:INFLAMMATORY BOWEL DISEASE 19; IBD19] [GWAS:Crohn's disease]
2x risk of Crohn's disease
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rs6596075 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.55 (CI 1.00-2.39), and for homozygotes, 2.06 (CI 1.35-3.14). [OMIM:INFLAMMATORY BOWEL DISEASE 5; [[IBD5]]]
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rs2371685 is in linkage disequilibrium with a polymorphism that increases susceptibility to Crohn's disease 1.56 times for carriers of the T allele
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Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. Unbiased estimation of odds ratios: combining genomewide association scans with replication studies. [PharmGKB:Non-Curated GWAS results: Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: 1,182 cases, 2,024 controls). This variant is associated with Crohn's disease.] [GWAS:Crohn's disease]
Increased risk for Crohn's Disease
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rs2631367, a SNP in the promoter region of the SLC22A5 gene, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is the more rare allele, which appears to be rs2631367(C).[Note: this orientation has not been confirmed relative to dbSNP.] A nearby SNP (rs1050152) in the coding region of the SLC22A4 gene defines a haplotype along with rs2631367, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%. [PharmGKB:Non-Curated No appreciable effect of this variant on carnitine disposition]
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
normal
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rs1050152, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T). A nearby SNP (rs2631367) in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%. [PharmGKB:Non-Curated Higher gabapentin exposure and lower renal clearance/tubular secretion in individuals carrying this variant] [OMIM:?]
normal
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rs9469220 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.14 (CI 0.98-1.32), and for homozygotes, 1.52 (CI 1.28-1.79). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: (see Parkes 2007); Risk Allele: rs9469220-A). This variant is associated with crohn's disease.] [GWAS:IgE levels] [GWAS:Crohn's disease]
Magnitude: 0
Frequency: 48.7%
References:8
Frequency: 48.7%
References:8
normal risk ankylosing spondylitis
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rs10865331 is a SNP in chromosomal region 2p15. After initial GWAS reports linked this SNP to ankylosing spondylitis (AS), a follow-up study in 456 Spanish patients replicated the association between the rs10865331(A) allele and higher risk for AS (p = 0.039). In a 2010 report, the AA genotype was associated with 1.3x odds of ankylosing spondylitis, and the GG genotype with 0.8x odds, compared to the AG genotype. [OMIM:?] [GWAS:Ankylosing spondylitis]
normal risk
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rs1343151 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.8 (p=1.0x10e-5). rs1343151 with rheumatoid arthritis (OR=1.14 [1.06-1.22], P=4x10-4) rs1343151 was '''not''' associated with rheumatoid arthritis in a study of 1,200+ Korean patients. A;A homozygous individuals showed a strongly reduced risk of Crohn's Disease compared those who were G;G homozygous. [PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This v...
common in complete genomics
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rs272893 and rs273900 are associated with Crohn's disease (OR 2.16; 95% CI 1.21-3.59 and OR 2.40; 95% CI 1.43-4.05)
0.5x decreased risk for endometriosis
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rs1800871(C) carriers are associated with a reduced endometriosis risk by approximately 2x compared with the common rs1800871(T;T) genotype in a study of 196 Chinese patients. rs2222202 (C/T) (p=0.03) and rs1800871 (C/T) (p=0.05) showed significant allelic associations with pediatric onset Crohn's disease. rs1800871(T) carriers were 3x more likely to have their pregnancies terminate early (<10 weeks) than (C) carriers, based on a study of ~500 pregnancies. In a study of 1,757 cases of Alzheimer's disease and 6,295 controls, an interaction was replicated between IL6 genotype rs2069837(A;A) and IL10 genotype rs1800871(C;C). The synergy factor (SF) was 1.63 (CI: 1.10-2.41, p = 0.01), controlling for age, gender and ApoE4 genotype. 23andMe reports that each G allele at rs1800871 is associat...
Magnitude: 0
Frequency: 70.8%
References:10
Frequency: 70.8%
References:10
normal
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rs17234657 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.54 (CI 1.34-1.76), and for homozygotes, 2.32 (CI 1.59-3.39). [OMIM:INFLAMMATORY BOWEL DISEASE 18; IBD18]
Magnitude: 0
Frequency: 76.1%
Repute:Good
References:2
Frequency: 76.1%
Repute:Good
References:2
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[GWAS:None]
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
normal
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rs6679677 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.98 (CI 1.72-2.27), and for homozygotes, 3.32 (CI 1.93-5.69). rs6679677 was also reported in the same study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.82 (CI 1.59-2.09), and for homozygotes, 5.19 (CI 3.15-8.55). Recently (Feb 2008), it has been asserted that the association between rs6679677 and type-1 diabetes is actually completely due to a closely linked, potentially causal variant identified as rs2476601, which is also known as Arg620Trp. In this study, apparently the largest to date, the odds ratio...
common in complete genomics
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rs2066844 is a SNP in the NOD2 gene; the SNP is also known as R702W or Arg702Trp, with the (C) allele encoding the Arg (R) and the (T) allele encoding the Trp (W). The two initial reports linking the minor(T) allele as strongly associated with Crohn's disease are and . rs2066844 is mentioned in as being strongly associated with Crohn's disease No association was found for NOD2/CARD15 SNPs (R702W, G908R) in Chinese patients with inflammatory bowel disease. [OMIM:CROHN DISEASE, SUSCEPTIBILITY TO]
normal
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rs2542151 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.3 (CI 1.14-1.48), and for homozygotes, 2.01 (CI 1.46-2.76). rs2542151 has been reported in the same study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.30 (CI 1.15-1.47), and for homozygotes, 1.62 (CI 1.17-2.24). In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.30 (CI 1.22–1.40). [PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide association study data identifies additional type 1 diabete...
normal
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rs4958847 is a SNP in the IRGM gene. A study of 507 CD patients, 475 UC patients and 576 controls from New Zealand Caucasians found that rs4958847, a SNP in the IRGM gene, was associated specifically with ileal Crohn's disease but not with other forms of inflammatory bowel disease. The reported odds ratio was 1.767, CI: 1.224-2.558, p=0.0022. Another study, including 557 Crohn's disease (CD) patients, 425 ulcerative colitis (UC) patients, and 672 ethnically matched Spanish controls as well as a meta-analysis concluded that rs4958847(A) was associated with CD (p=2.78 x 10(-17), pooled odds ratio 1.31) and UC (p=0.014, pooled odds ratio 1.13). Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease. Gene variants influencing measures of i...
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[GWAS:Crohn's disease]
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[GWAS:None]
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NOTE: information for rs1050152 was accidentally entered for this SNP, rs3792876. Although the SNPs are in the same gene, the original reference does not specifically refer to rs3792876 and the degree of linkage has not been confirmed. rs1051052, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T). A nearby SNP in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. rs2073838 and rs3792876 replicated for rheumatoid arthritis in Japanese, but not Caucasian populations. rs3792876 faile...
normal
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rs8111071 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.47 (CI 1.25-1.73), and for homozygotes, 1.28 (CI 0.56-2.88). [GWAS:None]
Magnitude: 0
Frequency: 84.1%
References:1
Frequency: 84.1%
References:1
normal Crohn's Disease risk
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Contribution of rs11465788 in IL23R gene to Crohn's disease susceptibility and phenotype in Chinese population. Found that T allele may be protective against Crohn's disease in Chinese.
Magnitude: 0
Frequency: 90.3%
Repute:Good
References:5
Frequency: 90.3%
Repute:Good
References:5
common in complete genomics
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[OMIM:INFLAMMATORY BOWEL DISEASE 19; IBD19] [GWAS:Crohn's disease]
Magnitude: 0
Frequency: 91.1%
Repute:Bad
References:28
Frequency: 91.1%
Repute:Bad
References:28
normal risk
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rs11465804 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.68 (p=0.0002). [PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This variant is associated with Crohn's disease.] [GWAS:Crohn's disease] [GWAS:Crohn's disease]
normal
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rs1000113 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.54 (CI 1.31-1.82), and for homozygotes, 1.92 (CI 0.92-4.00). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: (see Parkes 2007); Risk Allele: rs1000113-T). This variant is associated with crohn's disease.] [GWAS:Crohn's disease]
common in complete genomics
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23andMe blog rs7714584(G) linked with an increased risk for Crohn's disease. Similar to rs13361189 [GWAS:None]
Magnitude: 0
Frequency: 92.9%
Repute:Good
References:23
Frequency: 92.9%
Repute:Good
References:23
normal
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rs13361189 is a SNP in the IRGM gene. A study including 557 Crohn's disease (CD) patients, 425 ulcerative colitis (UC) patients, and 672 ethnically matched Spanish controls as well as a meta-analysis concluded that rs13361189(C) was associated with CD (p=1.07 x 10(-19), pooled odds ratio 1.34) and UC (p=0.0069, pooled odds ratio 1.16). 23andMe blog Each copy of a C at rs13361189 increases a person's risk of developing Crohn's disease 1.33 times compared to someone with two copies of a T [PharmGKB:Non-Curated GWAS results: Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: 1,182 cases, 2,024 controls). This variant is associated with Crohn's...
Magnitude: 0
Frequency: 94.7%
References:1
Frequency: 94.7%
References:1
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The top ranked interaction in the Crohn's disease data is between rs7154773 and rs10130695. The individual p-values are 0.004 and 0.476, respectively, while the signi?cance level of their interaction is 4.435E-43.
Magnitude: 0
Frequency: 94.7%
Repute:Good
References:7
Frequency: 94.7%
Repute:Good
References:7
Magnitude: 0
Frequency: 95.3%
Repute:Good
References:14
Frequency: 95.3%
Repute:Good
References:14
common in complete genomics
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blog summary of says :The exonic SNP c.313C>T (rs10065172) is in perfect linkage disequilibrium (r2=1.0) with a deletion polymorphism of 20 kbp mapping upstream of the IRGM gene. This deletion has been strongly associated with Crohn's disease in several European populations or those with European ancestry. [OMIM:IMMUNITY-RELATED GTPase FAMILY, M; IRGM]
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asthma related This SNP is in the promoter region of the IL-13 gene PMID: 17615386 IL-13 is involved in pulmonary inflammation, remodeling and susceptibility to chronic obstructive pulmonary disease (COPD). This IL13 promoter polymorphism may modulate the adverse effects of cigarette smoking on pulmonary function in long-term cigarette smokers. Every 20 pack-year increment in smoking was associated with a 2.4% reduction in mean ppFEV1(forced expiratory volume in 1 second, a measure used to assess lung disease, like COPD) in the common homozygous (CC) or heterozygous (CT) promoter genotypes, and an 8.2% reduction in mean ppFEV1 in minor allele homozygotes (TT, recessive model). *pack-year= packs per day x years smoked rs1800925 and/or rs11568506 related to psoriasis and/or Crohn's disease ?...
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rs2066847 is one of several SNPs referring to a one base insertion into a run of C's within exon 11 of the NOD2 gene; the other SNPs are rs5743293 and rs112436597. The two initial reports linking this insertion variant with Crohn's disease are and . In OMIM, this insertion is allelic variant #605956.0001 [GWAS:Crohn's disease]
common in complete genomics
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rs272893 and rs273900 are associated with Crohn's disease (OR 2.16; 95% CI 1.21-3.59 and OR 2.40; 95% CI 1.43-4.05)
common in complete genomics appears to be common on the 23andMe platform
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rs2066845 is a SNP in the NOD2 gene; this SNP is also known as G908R or Gly908Arg, with the (G) allele encoding the Gly (G) and the (C) allele encoding the Arg (R). The two initial reports linking the minor(C) allele as strongly associated with Crohn's disease are and . rs2066845 has also been reported, with an odds ratio of 3.5 (CI 1.51–7.01), to be associated with psoriatic arthritis. No association was found for NOD2/CARD15 SNPs (R702W, G908R) in Chinese patients with inflammatory bowel disease. [OMIM:CROHN DISEASE, SUSCEPTIBILITY TO]
149 snps
(hide) Cystic Fibrosis
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Formerly known as the very well studied rs1982073 [PharmGKB:Curated In conjunction with polymorphism at codon 25, defines high-, medium- or low-producer haplotype; Pro allele has been associated with higher levels of circulating TGFB1; Cystic Fibrosis patients who are C homozygotes may have increased risk of severe pulmonary disease; association found of C allele with increased risk of invasive breast cancer; associated with bone mineral density and genetic susceptibility to osteoporosis in Japanese adolescents and postmenopausal women; C allele may be involved in development of EBV-related diseases;C allele associated with increased risk for esophageal squamous cell carcinoma in Chinese; T allele associated with familial vesicoureteral reflux; C allele associated with increased severity ...
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In 'Association of the ADRA2A polymorphisms with the risk of type 2 diabetes: a meta-analysis.' a meta-analysis of publications prior to September 2012 showed no overall association between rs553668 and T2D risk, but did find an association with very high (poor) P-value for Europeans under recessive gene model (GT=AA, OR=1.36, p=0.02, 95% CI: 1.05, 1.76). In 'Genetic association of adrenergic receptor alpha 2A with obesity and type 2 diabetes.' rs553668 was found to correlate with obesity in Swedish population, but not significantly for BMI-corrected T2D risk. ADRA2A is involved in sympathetic nervous system's inhibition of insulin secretion and lipolysis, so direct effect on T2D is usually sought, but the Swedish study suggest it could work through body mass. It also mentions that rs55366...
Frequency: 28.3%
References:1
References:1
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[GWAS:None]
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23andMe blog cystic fibrosis having the CT genotype at rs7817 showed worse lung function than people with either two Cs or two Ts at this SNP. Identification of IFRD1 as a modifier gene for cystic fibrosis lung disease. [OMIM:INTERFERON-RELATED DEVELOPMENTAL REGULATOR 1; IFRD1]
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[GWAS:None]
Frequency: 38.9%
References:1
References:1
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[GWAS:None]
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this snp modulates cystic fibrosis disease severity
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Cystic Fibrosis rs1800123
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Cystic Fibrosis rs77101217
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Cystic Fibrosis rs74551128
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Cystic Fibrosis rs121908757
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Cystic Fibrosis rs267606722
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Cystic Fibrosis rs397508393
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Cystic Fibrosis rs121909012
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Cystic Fibrosis rs121909013
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Cystic Fibrosis rs79850223
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Cystic Fibrosis rs121909017
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Cystic Fibrosis rs121909019
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Marked as pathogenic for Cystic Fibrosis in ClinVar, but not listed at all in CFTR2 rs76879328
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Cystic Fibrosis rs121909026
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Cystic Fibrosis rs121908798
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Cystic Fibrosis rs76554633
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Cystic Fibrosis rs75115087
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Cystic Fibrosis rs121908765
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Cystic Fibrosis rs121908764
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Cystic Fibrosis rs74503330
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Cystic Fibrosis rs121909041
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Cystic Fibrosis rs267606723
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Cystic Fibrosis rs121909034
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Cystic Fibrosis rs121909047
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Cystic Fibrosis rs397508761
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Cystic Fibrosis rs397508163
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Cystic Fibrosis rs121908785
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Cystic Fibrosis rs397508174
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Cystic Fibrosis rs397508176
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Cystic Fibrosis rs397508183
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Cystic Fibrosis rs397508192
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Cystic Fibrosis rs397508200
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Cystic Fibrosis rs397508205
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Cystic Fibrosis rs397508227
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Cystic Fibrosis rs193922503
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Cystic Fibrosis rs121908755
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Cystic Fibrosis rs397508251
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Cystic Fibrosis; significance of this allele is unclear rs193922504
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cystic fibrosis rs75549581
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Cystic Fibrosis rs80055610
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Cystic Fibrosis rs121908794
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Cystic Fibrosis rs121908748
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Cystic Fibrosis rs121908812
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cystic fibrosis rs121908799
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Cystic Fibrosis rs397508350
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Cystic Fibrosis rs397508353
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Cystic Fibrosis rs374946172
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Cystic Fibrosis rs145449046
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Cystic Fibrosis rs387906359
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Cystic Fibrosis rs397515498
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Cystic Fibrosis rs397508387
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Cystic Fibrosis rs397508394
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Cystic Fibrosis rs397508399
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Cystic Fibrosis rs149790377
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Cystic Fibrosis rs397508435
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Cystic Fibrosis rs397508442
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Cystic Fibrosis rs397508447
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Cystic Fibrosis rs397508453
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Cystic Fibrosis rs141033578
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Cystic Fibrosis rs397508477
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Cystic Fibrosis rs397508477
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cystic fibrosis rs76151804
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Cystic Fibrosis rs150212784
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Cystic Fibrosis rs397508510
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Cystic Fibrosis rs142394380
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Cystic Fibrosis rs200321110
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Cystic Fibrosis rs202179988
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Cystic Fibrosis rs186045772
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Cystic Fibrosis rs139304906
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Cystic Fibrosis rs397508538
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Cystic Fibrosis rs75541969
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Cystic Fibrosis rs387906378
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Cystic Fibrosis rs121908763
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Cystic Fibrosis rs397508587
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Cystic Fibrosis rs121908783
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Cystic Fibrosis rs387906369
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Cystic Fibrosis rs121908784
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Cystic Fibrosis rs121908789
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Cystic Fibrosis rs121908808
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Cystic Fibrosis rs397508675
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Cystic Fibrosis rs397508702
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Cystic Fibrosis rs397508706
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Cystic Fibrosis rs121908788
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Cystic Fibrosis rs141158996
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Cystic Fibrosis rs74767530
References:0
normal
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rs213950, a SNP in the cystic fibrosis CFTR gene (but not one that is linked to cystic fibrosis), has been reported in a large study to be associated with type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.09 (CI 1.04–1.15). [OMIM:CFTR POLYMORPHISM]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
common in clinvar
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Cystic fibrosis; c.3808G>A, p.Asp1270Asn; of varying clinical consequence according to CFTR2 database named i5012029 by 23andMe [OMIM:VAS DEFERENS, CONGENITAL BILATERAL ABSENCE OF]
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also known as rs113993960 i3000001 is one of 23andMe's names for the Cystic Fibrosis Delta F508 mutation
normal
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also known as rs75527207 there is a specific medicine to treat this form of cystic fibrosis http://www.reuters.com/article/2012/01/31/us-fda-vertex-kalydeco-idUSTRE80U1JA20120131
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Cystic Fibrosis rs80034486
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previously considered predictive of Cystic Fibrosis, 23andMe has removed it from their reports as unreliable.
normal
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Cystic fibrosis (CF) is the most common autosomal recessive disorder in populations with European ancestry: the average carrier frequency is 1:25. It is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). The CFTR gene encodes a chloride transporter, gated by ATP binding and hydrolysis. It regulates the transport of chloride and other ions across the cell membrane. Mutations in CFTR result in raised sweat chloride, respiratory infections, and pancreatic insufficiency. To date, 1939 mutations in the CFTR gene that cause cystic fibrosis have been curated in the Cystic Fibrosis Mutation Database. Different combinations of mutations in the gene have different effects on its function and thus cause different disease phenotypes. The most common mutation is...
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Cystic Fibrosis rs121908747
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previously considered predictive of Cystic Fibrosis, 23andMe has removed it from their reports as unreliable.
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Cystic Fibrosis Known as rs121908789 outside of 23andMe.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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rs113993959, also known as G542X, is a SNP in the CFTR cystic fibrosis gene. This mutation is fairly rare, but in Ashkenazi Jews it accounts for ~13% of all cases of cystic fibrosis. See also OMIM 602421.0009. In 23andMe, rs113993959 may be called one of several names: i4000300, i5006109 or i5011314. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Cystic fibrosis; c.2125C>T, p.Arg709Ter named i5011500 by 23andMe
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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Cystic fibrosis; c.2290C>T, p.Arg764Ter named i5011532 by 23andMe
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Cystic fibrosis; c.1647T>G, p.Ser549Arg named i5011325 and i4000302 by 23andMe [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Cystic fibrosis; c.1000C>T, R334W or Arg334Trp named i4000296 by 23andMe, and also i5006070 and i5011077 aka R334W or Arg334Trp [OMIM:?]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
common in complete genomics
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rs28929474, also known as Glu342Lys as well as E366K, is a SNP in the serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 SERPINA1 gene. This SNP is the one most frequently leading, when homozygous, to the complications of alpha-1 antitrypsin deficiency and the associated high risk of emphysema and liver disease. Between 1 - 2% of US Caucasians are thought to be (heterozygous) carriers for this SNP, leading some associations, like the Alpha-1 Foundation, to call for mass carrier screening. * 23andMe blog rs28929474(T) increases odds of liver disease in cystic fibrosis patients by 4.17 times. (T;T) at both copies of this SNP causes alpha-1 antitrypsin deficiency; note use of opposite strand nomenclature by this company. Genetic polymorphisms and susceptibilit...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Known as I148T or Ile148Thr, rs35516286 was initially thought to thought to be a mutation associated with cystic fibrosis. However, as reported succinctly in the CFTR2 database, it is now believed that rs35516286 is only associated with cystic fibrosis CF when another mutation (usually rs121908767, aka 3199del6) is present on the same copy of the CFTR gene AND there is another CF-causing mutation on the other copy of the CFTR gene (i.e. the other chromosome). In other words, while rs35516286 may be co-inherited with a true-CF-causing variant, rs35516286 itself is not CF-causing.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Cystic fibrosis; c.3718-2477C>T named i5011981 and i4000325 by 23andMe [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Cystic fibrosis; c.2988+1G>A named i5011728, i6056297 and i4000321 by 23andMe Improved detection of cystic fibrosis mutations in the heterogeneous U.S. population using an expanded, pan-ethnic mutation panel. Clinical practice and genetic counseling for cystic fibrosis and CFTR-related disorders.
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
common in clinvar
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. Known primarily as G551D (although sometimes also called G511D) and also known as i4000305 by 23andMe, rs75527207 is a rare variant in the cystic fibrosis CFTR gene is thought to be present in ~1,200 patients in the US. The risk allele is rs75527207(A). G551D is termed a 'gating mutant', and is considered to be a somewhat different class of cystic fibrosis mutation compared to variants that lead to misfolded proteins. Like almost all cystic fibrosis variants, individuals must inherit two defective CFTR alleles to manifest the disease; since G551D is ~20 times rarer than the most common CFTR variant, deltaF508, patients carrying one G551D variant are likely to be compound heterozygotes harboring an additional CFTR variant. In early 2012, the biotech company Vertex Pharmaceutics received F...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Cystic fibrosis; c.254G>A, G85E or Gly85Glu named i4000294 by 23andMe [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs76713772, also known as 1717-1G->A or 1585-1G>A, is a SNP in the CFTR gene considered pathogenic for cystic fibrosis. In 23andMe, rs76713772 goes by several names: i4000317, i5011301 and i6056292. Mutation spectrum in Jewish cystic fibrosis patients in Israel: implication to carrier screening. [OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
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Cystic fibrosis; c.579+1G>T named i4000315 and i5010951 by 23andMe
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Cystic fibrosis; c.1013C>T, Thr338Ile or T338I named i5006102, i5011083, and i5053827 by 23andMe [OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
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Cystic fibrosis; c.349C>T, Arg117Cys or R117C named i5010836 by 23andMe, but i5010835 at this same position represents the C>G change (rather than the C>T)
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Cystic fibrosis; c.3196C>T, p.Arg1066Cys named i5006085, i5053836 and i6008913 by 23andMe [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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This cystic fibrosis variant, c.350G>A, known as Arg117His or R117H and associated with a G>A mutation, is reported to have varying clinical consequences. Other mutations possible at this position are G>C (Arg117Pro) and G>T (Arg117Leu), but their effect is not listed in ClinVar or CFTR2. rs78655421 is also named i5010839, i5006049 and i4000295 by 23andMe; while for them, i5010838 represents the G>C mutation and i5010837 the G>T. [OMIM:?]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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rs78756941, also known as 621+1G>T or 489+1G>T, is a SNP in the CFTR gene considered pathogenic for cystic fibrosis. 23andMe has at least three terms in use for rs78756941: i4000314, i5010909 and i6056291.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Cystic fibrosis; c.2668C>T, p.Gln890Ter names used by 23andMe for this SNP include: i5006113, i5011627 and i5053834 [OMIM:?]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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rs80224560, probably best known as 2789+5G>A, is a mutation in the cystic fibrosis CFTR gene. It has been reported as leading to a relatively mild form of cystic fibrosis; see the discussion at I4000320. also named i5011620 by 23andMe
common in complete genomics
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rs17580, also known as the S or PiS allele, is a SNP in the SERPINA1 gene. Levels of alpha-1 antitrypsin (encoded by the SERPINA1 gene) may be reduced in carriers of the rs17580(T) allele, but there is no known association with liver disease or cystic fibrosis. The rs17580 PiS variant is most associated with risk of developing COPD, especially in smokers, but it's association with emphysema is variable. See rs28929474 for the most common pathologic SNP (PiZ) in the SERPINA1 gene. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is T, but test results may be in the plus orientation where the risk allele is A (although currently 23andMe reports the risk allele as T). This SNP has an ambiguous flip which can make...
common in clinvar
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Cystic fibrosis; c.3302T>G, p.Met1101Arg named i5011864 by 23andMe
common in clinvar
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Cystic fibrosis; c.366T>A, Tyr122Ter or Y122X named i5010848 by 23andMe
common in clinvar
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Cystic fibrosis; c.3909C>G, p.Asn1303Lys; note orientation is minus in dbSNP and SNPedia named i5012079 and i4000311 by 23andMe [OMIM:?]
172 snps
(hide) Deafness
Frequency: 30.8%
References:1
References:1
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[OMIM:?]
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deafness [OMIM:DEAFNESS, AUTOSOMAL DOMINANT 4; DFNA4]
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rs180275(G) associated with increased risk of sudden deafness in Korean population. odds ratio (OR) for SD associated with the G vs. A allele was 2.58 rs180275 G allele protective against an increase in BMI in Korean population.
common in complete genomics
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deafness [OMIM:SEIZURES, SENSORINEURAL DEAFNESS, ATAXIA, MENTAL RETARDATION, AND] [GWAS:None]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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deafness [OMIM:DEAFNESS, AUTOSOMAL DOMINANT NONSYNDROMIC SENSORINEURAL 3]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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deafness [OMIM:DEAFNESS, AUTOSOMAL DOMINANT NONSYNDROMIC SENSORINEURAL 6]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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deafness [OMIM:DEAFNESS, AUTOSOMAL DOMINANT NONSYNDROMIC SENSORINEURAL 4]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:10
Repute:Good
References:10
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
23 snps
(hide) Deep vein thrombosis
Frequency: 16.5%
References:2
References:2
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. *rs13146272 in CYP4V2 (risk allele frequency, 0.64) OR 1.24 (95% CI, 1.11-1.37) for rs13146272 *rs2227589 in SERPINC1 (risk allele frequency, 0.10) OR 1.29 (95% CI, 1.10-1.49) for rs2227589 *rs1613662 in GP6 (risk allele frequency, 0.84) OR 1.15 (95% CI, 1.01-1.30) for rs1613662 A study of 453 VTE cases and 1,327 controls was able to replicate the 'mild effects' of this SNP on risk for VTE, however they felt that stronger associations were found between increased VTE risk and either the Factor V Leiden mutation (rs6025)or having blood types O or A2. An evaluation of candidate genes of inflammation and thrombosis in relation to the risk of venous thromboembolism: The W...
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. rs2227589 in SERPINC1 (risk allele frequency, 0.10) OR 1.29 (95% CI, 1.10-1.49) associated with plasma anti-FXa activity and antithrombin levels: carriers of the A allele had slightly but significantly lower anticoagulant activity and levels than GG subjects (97.0+/-7.3% vs. 94.6+/-8.4%; p=0.032; 99.5+/-5.8% vs. 94.8+/-5.6%; p=0.001; respectively)
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. per risk allele odds ratio *rs13146272 in CYP4V2 (risk allele frequency, 0.64) OR 1.24 (95% CI, 1.11-1.37) for rs13146272 *rs2227589 in SERPINC1 (risk allele frequency, 0.10) OR 1.29 (95% CI, 1.10-1.49) for rs2227589 *rs1613662 in GP6 (risk allele frequency, 0.84) OR 1.15 (95% CI, 1.01-1.30) for rs1613662 A study of 453 VTE cases and 1,327 controls was able to replicate the 'mild effects' of this SNP on risk for VTE, however they felt that stronger associations were found between increased VTE risk and either the Factor V Leiden mutation (rs6025)or having blood types O or A2. An evaluation of candidate genes of inflammation and thrombosis in relation to the risk of ve...
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis.
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. Explaining variability in ciclosporin exposure in adult kidney transplant recipients. Polymorphisms in NF-kappaB, PXR, LXR, PPARgamma and risk of inflammatory bowel disease. Pregnane X receptor (PXR/NR1I2) gene haplotypes modulate susceptibility to inflammatory bowel disease. Variants of the human NR1I2 (PXR) locus in chronic periodontitis.
common
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. [OMIM:?]
6 snps
(hide) Dementia
Women have lower risk of Endometriosis but normal risk for Endometrial Cancer, and more cognitive impairment with age. Men have zero risk, but can pass this on to their daughters. This is the normal version of Estrogen Receptor 1 (alpha). It has more cognitive decline than the rare version, with old women only remembering half as much details on the East Boston Memory Test immediate recall test.
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rs9340799 is a SNP in the estrogen alpha receptor ESR1 gene, and it is also known as the -351A>G variant. Among women, rs8179176, rs9340799, rs1256065, and rs1256030 were associated with likelihood of developing cognitive impairment with ageing. In men, rs728524, rs1255998, and rs1256030 were associated with cognitive impairment. A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs9340799) and risk of ischemic stroke. A study of 702 cases with invasive endometrial cancer concluded that the less common alleles of SNP rs9340799 lowered risk for the disease. The odds ratio was 0.75 (CI: 0.60-0.93) for (A;G) and 0.53 (CI: 0.37-0.77) for (G;G) compared to rs9340799(A;A) individuals. Endometriosis Uterine Fibroids [PharmGKB:Curated SNP i...
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
2 snps
(hide) Depression
1.3x increased risk for depression
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In Caucasian non-Hispanics, the rs1360780(T) allele is associated with increased risk for depression, with an odds ratio of 1.39 (CI: 1.14-1.70, p=0.046). This same SNP, which is in the FKBP5 gene, may influence how patients respond to antidepressants including citalopram. rs1360780(T;T) homozgyotes tend to report more depressive episodes, but they also respond better to treatment with antidepressants. rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing. [PharmGKB:Curated This variant is associated with higher chance of response to anti-depressant drugs.] [OMIM:FK506-BINDING PROTEIN 5; FKBP5]
Normal (higher) risk of ADHD symptoms. This is one normal and one rare form of the CLOCK gene. In addition to possibly affecting evening preference, it has been linked to normal Attention Deficit Hyperactivity Disorder symptom scores.
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rs1801260, a SNP in the CLOCK gene known as 3111 T/C, has been reported to influence sleep and activity patterns in patients affected by bipolar depression. From this article's abstract: 'Compared to T/T homozygotes, carriers of the C allele had a similar degree of severity of depression, but showed higher activity levels in the evening, a delayed sleep onset (mean 79 min later), and a reduced amount of sleep during the night (mean 75 min less).' Allele frequencies of T3111C SNP of hClock were significantly different between schizophrenics and controls (chi(2) = 19.738, P < 0.05). Schizophrenics had a significantly higher frequency of the C allele compared with controls (OR = 2.613, 95% CI = 1.693-4.034). (Han Chinese population.) There was a strong, significant association (P < 0.00...
Increased risk of mental disorders
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rs16944 is a SNP in the interleukin 1, beta gene, a member of the cytokine family involved in the inflammatory response. The rs16944 G;G genotype is associated with risk for multiple mental illnesses. An increased risk for schizophrenia was found in a genetic association study of 2111 Caucasian individuals with an odds ratio of 1.24 (95% CI 1.09, 1.41) . Studies examining the brains of schizophrenic and bipolar individuals found reduced gray matter and hypoactivity associated with the G;G genotype. Additionally, this genotype is associated with impaired ability to achieve remission in a study of 256 Caucasian individuals with depression (odds ratio = 1.74; 95% confidence interval 1.2-4.3). The rs16944 A allele increases susceptibility to Osteoarthritis, with 1.80 times for heterozygotes (A...
7x more likely to respond to certain antidepressants. This version of a blood brain barrier protein allows many common antidepressants to enter the brain, including: amitriptyline (Elavil), citalopram (Celexa), paroxetine (Paxil), and venlafaxine (Effexor). That makes those antidepressants 7 times more effective.
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rs2032583 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2032583 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
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[OMIM:CHOLINERGIC RECEPTOR, MUSCARINIC, 2; CHRM2]
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[GWAS:Major depressive disorder]
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Association between rs2799573 and psychiatric disorders was shown in a 2013 study by the Cross-Disorder Group of the Psychiatric Genomics Consortium . In this study, genome-wide SNP data consisting of 1,250,922 autosomal SNPs were analyzed to identify genetic variants associated with autism spectrum disorder, ADHD, bipolar disorder, major depressive disorder, and schizophrenia. 33,332 cases and 27,888 controls included both unrelated and family-based samples (trios). A multinomial logistic regression procedure was used to identify the best-fitting model of relations between genotype and phenotype. This SNP, on chromosome 10 in an intron of CACNB2, was one of four genome-wide significant signals associated with the five psychiatric disorders (p = 4.29 x 10-8). The risk allele T exhibited al...
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[OMIM:CHOLINERGIC RECEPTOR, MUSCARINIC, 2; CHRM2]
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder (broad)]
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[GWAS:Major depressive disorder]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of recurrent major depressive disorder in two European case-control cohorts. (Initial Sample Size: 1,359 cases, 1,782 controls; Replication Sample Size: NR); (Region: 12p13.32; Reported Gene(s): CCND2; Risk Allele: rs4238010-G); (p-value= 0.000006).This variant is associated with Major depressive disorder.] [GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
~10% more likely to respond to citalopram
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rs1954787, located in an intron of the GRIK4 gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From the abstract of this article: 'The effect size of (this) GRIK4 marker alone was modest, but homozygote carriers of the treatment-response-associated marker alleles of both the GRIK4 and HTR2A (see rs7997012) genes were 23% less likely to experience nonresponse to (citalopram) treatment relative to participants who did not carry any of these marker alleles.' * See also Anxiety Blog posting [PharmGKB:Curated A study in 1,816 eligible patients from the STAR*D cohort found that genetic variation in a kainic acid-type glutamate receptor is reproducibly associated with response to the antidepressant citalopr...
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rs211105, rs1800532 and rs7933505 related to schizophrenia [OMIM:TRYPTOPHAN HYDROXYLASE 1; TPH1]
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[GWAS:Major depressive disorder]
Frequency: 27.4%
Repute:Good
References:3
Repute:Good
References:3
7x more likely to respond to certain antidepressants
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rs12720067 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs12720067 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are kn...
7x more likely to respond to certain antidepressants
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rs2235040 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2235040 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
normal risk for depression
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rs2156921, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for depression. The odds ratio for carriers of the minor allele (G) are reported as 1.29 (p=0.031) based on a study of 329 Japanese patients.
7x more likely to respond to certain antidepressants
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rs7787082 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs7787082 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
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[GWAS:Major depressive disorder]
more resistant to treatment for depression
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Based on a study of 256 Caucasian patients being treated for depression, carriers of a rs1049353(G) allele were less likely to respond favorably, particularly if they were females with comorbid anxiety. rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. No evidence for an involvement of variants in the cannabinoid receptor gene (CNR1) in obesity in German children and adolescents. The G1422A variant of the cannabinoid receptor gene (CNR1) is associated with abdominal adiposity in obese men. No association of...
~18% less likely to respond to citalopram
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rs7997012, located in an intron of the HTR2A gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From this article : 'HTR2A encodes the serotonin 2A receptor, which is downregulated by citalopram. Participants who were homozygous for the A allele had an 18% reduction in absolute risk of having no response to treatment, compared with those homozygous for the other allele.' * See also Anxiety Blog posting [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: Patients with the 5-HTR2A intron 2 (rs7997012) AA genotype suffered from more pronounced side effects compared to carriers of the GA or GG genotype. Study size: 124. Study population/ethnicity: Caucasian; Patients with psychiatric diso...
Frequency: 40.7%
References:1
References:1
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
Frequency: 45.1%
References:1
References:1
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
Frequency: 46.4%
References:1
References:1
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
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Trajectories of change in depression severity during treatment with antidepressants. Pharmacogenomics of antidepressant drugs.
Frequency: 54.0%
References:1
References:1
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism.
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism.
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism.
Frequency: 69.6%
References:1
References:1
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder (broad)]
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder (broad)]
Frequency: 80.4%
References:1
References:1
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[GWAS:Major depressive disorder]
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[GWAS:Major depressive disorder]
References:1
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism.
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commonly referred to as A779C Only for Hispanics, individuals who have a genoset composed of rs1799913(C;C) and rs7963720(T;T) are reported to be at 14x higher risk for developing heroin addiction (CI:0.83-244.63, p=0.012). Again, only for Hispanics, individuals having a genoset composed of rs1799913(C;C) and rs4290270(T;T) are reported to be at 9x higher risk for developing heroin addiction (CI:0.5-153, p=0.063). Association between 5-HT2A, TPH1 and GNB3 genotypes and response to typical neuroleptics: a serotonergic approach. Tryptophan hydroxylase gene 1 (TPH1) variants associated with cerebrospinal fluid 5-hydroxyindole acetic acid and homovanillic acid concentrations in healthy volunteers. [OMIM:TRYPTOPHAN HYDROXYLASE 1; TPH1]
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism. Associations of glutamate decarboxylase genes with initial sensitivity and age-at-onset of alcohol dependence in the Irish Affected Sib Pair Study of Alcohol Dependence. Heroin addiction in African Americans: a hypothesis-driven association study.
possible weight gain if taking olanzapine
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rs3813929, also known as -759C/T, is a SNP in the 5-hydroxytryptamine (serotonin) receptor 2C HTR2C gene. A study of 107 patients with schizophrenia being treated with olanzapine reported a protective effect against weight-gain from the (T) allele of this SNP; zero patients (of 28) with a rs3813929(T) allele had a body mass index increase of >=10% (p=0.002), whereas (C;C) homozygotes did. This effect may also involve nearby SNP rs518147. T allele showed borderline significant association with higher BMI and incidence of lifetime major depressive disorder among 4978 persons from the European Prospective Investigation into Cancer (EPIC)-Norfolk study, however, only the association with BMI remained borderline significant within the full EPIC-Norfolk cohort (20,981 persons) The association...
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[GWAS:Major depressive disorder]
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Association between glutamic acid decarboxylase genes and anxiety disorders, major depression, and neuroticism.
normal
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rs1545843 is one of two linked SNPs potentially associated (at a distance though) with the SLC6A15 gene; the other is rs1031681. A GWAS study and meta-analysis ultimately including six independent samples, primarily Caucasion/European but also including an African-American sample, found that the rs1545843(A) allele was associated with higher risk for major depression, but only in individuals less than 55 years old and only when homozygous, with an odds ratio of 1.4 (p = 2 x 10e-8).
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
common/normal Val/val (normal) variant of the Val66Met snp in the BDNF gene that codes for brain-derived neurotrophic factor. Met/met is associated with susceptibility to neuropsychiatric disorders.
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
normal
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rs2267013, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for depression. The odds ratio for carriers of the minor allele (G) are reported as 1.27 (p=0.044) based on a study of 329 Japanese patients.
Magnitude: 0
Frequency: 84.6%
Repute:Good
References:1
Frequency: 84.6%
Repute:Good
References:1
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:1
Frequency: 85.0%
Repute:Good
References:1
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[GWAS:Major depressive disorder]
higher risk for RA
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rs6314, also known as C1354T or His452Tyr/H452Y, is a SNP in the serotonin 2A receptor HTR2A gene. Based on a study of 166 Caucasian patients being treated for depression with paroxetine, rs6314 heterozygotes were associated with better response. There was a significantly higher frequency of heterozygotes in the remitter and response groups in comparison to the non-remitter (odds ratio 7.50, p=0.002) and non-response groups (odds ratio 5.25, p=0.01). * rs6314 is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6314(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs13286...
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:1
Frequency: 88.5%
Repute:Good
References:1
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[GWAS:Major depressive disorder]
Magnitude: 0
Frequency: 91.2%
Repute:Good
References:1
Frequency: 91.2%
Repute:Good
References:1
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[GWAS:Major depressive disorder]
Magnitude: 0
Frequency: 91.2%
References:2
Frequency: 91.2%
References:2
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[GWAS:Major depressive disorder (broad)]
normal
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rs5558 (F528C) is a non-synonymous SNP in SLC6A2 (norepinephrine transporter), with a T encoding for Phenylalanine and C encoding the rare Cysteine variant. assoc. w/ major depression Cysteine variant exhibited increased norepinephrine transport, insensitivity to protein kinase C induced down-regulation, and a decrease in desipramine (tricyclic antidepressant) potency
common for Caucasians on the 23andme platform
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rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission paper Association with and bipolar disorder in a Northern Swedish, Isolated Population. 182 patients and 364 unrelated control individuals. P = .001 rs11178997 significantly reduced TPH2 transcriptional activity by 22% and 7% in cell lines might have implications for the development and function of the serotonergic system in the brain. paper Carriers of the A-Allele of rs11178997 showed a decreased cortisol and ACTH stimulation. might be crucial factors for major depression pdf paper associated with bipolar disorder Minor allele yielded odds ratio of 1.5 (CI:1.2-1.9) for increased risk for bipolar disorder in a study of 883 Russian patients. Transmission disequilibrium of polymorphic variants in the tryp...
73 snps
(hide) Diabetes
some risk linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil).
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
Magnitude: 2
Frequency: 50.0%
Repute:Bad
References:77
Frequency: 50.0%
Repute:Bad
References:77
1.3x risk for Heart Attack. Normal risk for Abdominal Aortic Aneurysm and Brain Aneurysm. One copy of an SNP that increases risk of Myocardial Infarction (Heart Attack) and other Coronary Heart Disease. It has been shown that regularly eating raw vegetables and fruit can reduce the risk to the same level as people without this SNP. This SNP also has the normal medium risk of abdominal aortic aneurysm (weakened artery to abdomen and legs) or brain aneurysm (weakened artery to brain).
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This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...
average response to metformin in type 2 diabetics
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rs4585 has been found to modify the metformin response in patients with type 2 diabetes. Metformin Response
1.4x increased risk for heart disease
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rs10757274 and rs2383206 can significantly increase the risk of heart diseaseAbout one in every four Caucasians are thought to carry the variants, and their risk of coronary heart disease is increased by 30 to 40%. rs10757278] in the same region has been linked to diabetes The chromosomal region where these SNPs are located is 9p21, and has no known genes. a [http://suicyte.wordpress.com/2007/05/26/soul-searching-i/ blog post about investigating rs10757274 and rs2383206 This SNP was also associated with increased risk for coronary artery disease in a Korean population. Also found to be significant in a study of 416 Italian myocardial infarction patients. A study of 1,000+ patients with early-onset angiographic coronary artery disease (CAD) concluded that rs2383206(G) was associated with an...
Frequency: 12.4%
References:34
References:34
if obese, dieting more effective
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rs17300539, also known as -11391 G/A, is a SNP in the promoter of the adiponectin ADIPOQ gene. A small study of 180 Spanish patients with obesity concluded that rs17300539(G;G) individuals are at increased risk of insulin resistance and MetS complications compared to carriers of an (A) allele. The rs17300539(A) allele confered protection from weight regain, particularly at 32-60 weeks after the low-calorie dietary intervention, when improvement in GG subjects had disappeared adiponectin levels and risk of diabetes rs17300539 P(n) = 2.6 x 10(-8) and rs822387 (P(n) = 3.8 x 10(-5) [OMIM:?]
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In 'Association of the ADRA2A polymorphisms with the risk of type 2 diabetes: a meta-analysis.' a meta-analysis of publications prior to September 2012 showed no overall association between rs553668 and T2D risk, but did find an association with very high (poor) P-value for Europeans under recessive gene model (GT=AA, OR=1.36, p=0.02, 95% CI: 1.05, 1.76). In 'Genetic association of adrenergic receptor alpha 2A with obesity and type 2 diabetes.' rs553668 was found to correlate with obesity in Swedish population, but not significantly for BMI-corrected T2D risk. ADRA2A is involved in sympathetic nervous system's inhibition of insulin secretion and lipolysis, so direct effect on T2D is usually sought, but the Swedish study suggest it could work through body mass. It also mentions that rs55366...
reduced risk of multiple myeloma
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A study of 219 female melanoma patients and an equal number of controls concluded that 4 linked SNPs within the IL6R gene were associated with increased melanoma risk, but only when heterozygous. The odds ratio associated with the minor allele of this SNP, rs8192284 (also known as Asp358Ala), was 1.68 (CI: 1.04-2.73). The 4 linked SNPs from identified in this study are: rs6684439, rs4845618, rs4845622, and rs8192284. linked to diabetes by multiple myeloma *rs1801278 [C/T versus C/C genotypes; OR, 4.3; 95% confidence interval (CI), 1.5-12.1] *rs6684439 (T/T versus C/C; OR, 2.9; 95% CI, 1.2-7.0) *rs7529229 (C/C versus T/T; OR, 2.5; 95% CI, 1.1-6.0) *rs8192284 (C/C versus A/A; OR, 2.5, 95% CI, 1.1-6.0) [OMIM:INTERLEUKIN 6 RECEPTOR; IL6R] [GWAS:Fibrinogen] [GWAS:C-reactive protein]
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association with type 1A diabetes (rs1233478, p=1.6x10(-23), allelic odds ratio=2.0)
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Affects type-2 diabetes popular in pubmed Variants in hepatocyte nuclear factor 4alpha are modestly associated with type 2 diabetes in Pima Indians. Single nucleotide polymorphisms of the HNF4alpha gene are associated with the conversion to type 2 diabetes mellitus: the STOP-NIDDM trial. Association of genetic variations near P2 promoter of the hepatocyte nuclear factor-4alpha gene and insulin secretion index in Thais. Studies in 3,523 Norwegians and meta-analysis in 11,571 subjects indicate that variants in the hepatocyte nuclear factor 4 alpha (HNF4A) P2 region are associated with type 2 diabetes in Scandinavians. Gene-gene interactions between HNF4A and KCNJ11 in predicting Type 2 diabetes in women. Evidence of interaction between PPARG2 and HNF4A contributing to variation in insulin se...
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This SNP may be related to obesity and diabetes. Genomic variants at the PINK1 locus are associated with transcript abundance and plasma nonesterified fatty acid concentrations in European whites. Near perfect linkage disequilibrium with rs622525. G allele is a proxy for rs622525(T) which is associated with higher PINK1 transcript levels.
Repute:Bad
References:38
References:38
~1.2x increased risk for heart disease
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rs10757274 is a SNP located in chromosomal region 9p21; to date (2009), it is the strongest genetic predictor of early myocardial infarction (heart attack) discovered so far. SNPs in this region are also associated with increased risk of stroke, abdominal aortic aneurysm (AAA), and intracranial aneurysm. Based on a large (20,000+) study primarily of Caucasian females, it appears that on its own, this single SNP does not improve on the discrimination or classification of predicted heart disease risk achieved by traditional risk factors, high-sensitivity C-reactive protein, and a family history of premature myocardial infarction. rs10757274 and rs2383206 can double the risk of heart diseaseAbout one in every four Caucasians are thought to carry the gene variants. rs10757278] in the same regi...
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This SNP may be related to obesity and diabetes. Genomic variants at the PINK1 locus are associated with transcript abundance and plasma nonesterified fatty acid concentrations in European whites. T allele associated with higher PINK1 transcript levels. Near perfect linkage disequilibrium with rs3131713.
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
30% higher risk of diabetes
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rs20417, also known as -765G>C, is a SNP in the Prostaglandin endoperoxidase synthase 2 PTGS2 gene. In a group of Pima Indians, individuals with the variant PTGS2 rs20417 CC genotype had a 30% higher Type 2 diabetes prevalence compared with subjects with the GG genotype rs20417 was not found to be associated with prostate cancer in a large case-control study (n(cases)=1608, n(controls)=3058), nor in a meta-analysis of 3 other studies. Data-mining analysis suggests an epigenetic pathogenesis for type 2 diabetes. Allellic variants in regulatory regions of cyclooxygenase-2: association with advanced colorectal adenoma. Polymorphisms of prostaglandin-endoperoxide synthase 2 gene, and prostaglandin-E receptor 2 gene, C-reactive protein concentrations and risk of atherothrombosis: a nested ca...
common in clinvar
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suggested the contribution of rs237025 to type-1 diabetes, however in this failed to replicate. This SNP is also known as Met55Val, M55V, or A163G. This was the first SNP in SNPedia. The type 1 diabetes susceptibility gene SUMO4 at IDDM5 is not associated with susceptibility to rheumatoid arthritis or juvenile idiopathic arthritis. Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. Evidence for the role of small ubiquitin-like modifier 4 as a general autoimmunity locus in the Japanese population. SUMO4 M55V variant is associated with diabetic nephropathy in type 2 diabetes. Association study of NFKB1 and SUMO4 polymorphisms in Chinese patients with pso...
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23andMe blog each G at rs4293393 decreased the odds of chronic kidney disease by 24%. Approximately 18% of people with European ancestry have at least one G at this SNP. DeCode reports that the T allele of rs4293393 is associated with kidney stones and chronic kidney disease. This SNP may also be associated with susceptibility to gout], hypertension, and diabetes.
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y or Cys282Tyr mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who act...
common in complete genomics
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One report based on a study of 480 Danish families indicated that the rs3772534 SNP in the CBLB gene indicated an increased risk for developing type 1 diabetes, and that there might be co-inheritance with the rs3087243 SNP found in the CTLA4 gene. However, a subsequent study based on over 2,000 parent-child trios (ie families) failed to find any evidence of either effect.
complex; generally normal risk
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rs361525 is also known as the TNF-238 SNP, and occasionally the rs361525(A) allele is referred to as 238.2 (with the more common (G) allele being 238.1). This SNP in the tumor necrosis factor-alpha gene has been linked to a wide variety of conditions: * Breast cancer ** A large study of over 5,000 Caucasian women found that rs361525(A) allele carriers were at somewhat elevated risk for breast cancer compared to the (G;G) genotype, with an odds ratio per allele of 1.18, CI: 1.04-1.35, p(trend)= 0.008. ** However, a 2009 European study of 30,000 breast cancer cases, compared to 30,000 controls, found no association, or as they put it, 'persuasive evidence against an overall association between invasive breast cancer risk and (this SNP)'. * Graft versus host disease (GVHD) ** A study of ~100 ...
19 snps
(hide) Drug abuse
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This SNP, located in the 3' UTR of the CSNK1E gene, has been associated with sensitivity to the acute effects of d-amphetamine. Sensitivity to psychoactive drugs has been associated with potential to develop drug abuse. The more sensitive allele is rs135745(C). However, in a separate study, this SNP did not affect susceptibility to methamphetamine dependence or psychosis, at least in a Japanese population. Note: orientation relative to dbSNP needs to be confirmed/checked.
normal
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rs324420 is a SNP, also known as Pro129Thr, in the fatty acid amide hydrolase FAAH gene, which has shown associations with some substance use disorders. rs324420(C) encodes the more common Pro, while the (A) allele encodes the Thr. Among 80 individuals with drug abuse or alcoholism and over 1,000 controls, the odds ratio for risk of problem drug or alcohol use among rs324420(A;A) individuals was 4.5 (CI: 2.2 - 8.4); the odds ratio for risk of street drug use was 2.2 (CI: 1.3–3.7); and the odds ratio for risk of combined street drug use and problem drug/alcohol use was 4.9 (CI: 2.5–9.7) When this study was pooled with the results of another study of 249 subjects with documented multiple different drug addictions compared to drug free individuals of the same ethnic backgrounds, t...
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located in promoter region of BDKRB2 - associated with panic disorder, bipolar disorder, and substance abuse Identification of functional SNPs in the 5-prime flanking sequences of human genes.
3 snps
(hide) Dupuytren's contracture
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
common in complete genomics
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rs7524102 increases susceptibility to Bone mineral density variations, lower for carriers of the A allele rs7524102 increases susceptibility to Osteoporotic fractures 1.12 times for carriers of the A allele Common variants in the region around Osterix are associated with bone mineral density and growth in childhood. Replication study of candidate genes/loci associated with osteoporosis based on genome-wide screening. OPG and RANK polymorphisms are both associated with cortical bone mineral density: findings from a metaanalysis of the Avon longitudinal study of parents and children and gothenburg osteoporosis and obesity determinants cohorts. Analysis of recently identified osteoporosis susceptibility genes in Han Chinese women. [PharmGKB:Non-Curated GWAS results: New sequence variants ass...
Magnitude: 0
Frequency: 90.9%
Repute:Good
References:2
Frequency: 90.9%
Repute:Good
References:2
8 snps
(hide) Dyslexia
Slightly increased dyslexia risk
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Rs807701, a SNP in the DCDC2 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (C). One study reports that the odds ratio for rs807701 genotypes increases if calculated from subsets of more severely dyslexic individuals as compared to more heterogenous, larger groups of dyslexic individuals. The genotype relative risk (GRR) for rs807701(C;C) increased from 1.88 (95% CI 0.89-3.97; P=.058) for the larger group up to 5.04 (95% CI 1.35-18.88; P=.002) for the most severely affected group. Combined with another SNP marker in the DCDC2 gene, rs793862, the (haplotype) GRR also increased for the homozygous haplotype rs793862(A)-rs807701(C), from 4.11 (95% CI 2.77-6.08; P<.0001) for the ...
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[OMIM:?]
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Further evidence that the KIAA0319 gene confers susceptibility to developmental dyslexia.
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Strong genetic evidence of DCDC2 as a susceptibility gene for dyslexia.
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[GWAS:Speech perception in dyslexia]
1.5x risk
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Rs4504469, a nonsynonymous SNP in exon 4 of the KIAA0319 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (T). The odds ratio in a study of case:control study of ~400 Caucasians associated with rs4504469(T) is 1.51 (CI: 1.17–1.95, p = 0.002). A 77-kilobase region of chromosome 6p22.2 is associated with dyslexia in families from the United Kingdom and from the United States. Strong genetic evidence of DCDC2 as a susceptibility gene for dyslexia. A common variant associated with dyslexia reduces expression of the KIAA0319 gene. Convergent genetic linkage and associations to language, speech and reading measures in families of probands with Specific Language Impai...
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plos linked to dyslexia A common variant associated with dyslexia reduces expression of the KIAA0319 gene. [OMIM:DYSLEXIA, SUSCEPTIBILITY TO, 2; DYX2]
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[OMIM:?]
higher risk for dyslexia
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The more common allele of rs3212236 has been linked to increased risk for developmental dyslexia in a study of ~300 British families. While odds ratios were not reported, the significance was reported as p=0.02.
increased dyslexia risk
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Rs793862, a SNP in the DCDC2 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (A). One study reports that the odds ratio for rs793862 genotypes increases if calculated from subsets of more severely dyslexic individuals as compared to more heterogenous, larger groups of dyslexic individuals. The genotype relative risk (GRR) for rs793862(A;A) increased from 3.15 (95% CI 1.30-7.66; P=.011) for the larger group up to 5.40 (95% CI 1.27-23.01; P=.002) for the most severely affected group. Combined with another SNP marker in the DCDC2 gene, rs807701, the (haplotype) GRR also increased for the homozygous haplotype A-C, from 4.11 (95% CI 2.77-6.08; P<.0001) for the larger group, up to ...
normal risk
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The more common allele of rs761100 has been linked to increased risk for developmental dyslexia in a study of ~300 British families. While odds ratios were not reported, the significance was reported as p=0.02. Convergent genetic linkage and associations to language, speech and reading measures in families of probands with Specific Language Impairment. Developmental Dyslexia
common
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genetic risk for poor reading performance. Rs2143340, a SNP in the TTRAP gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the US/UK Caucasian populations studied is (C), and it is indicative of a risk haplotype found in ~18% of the general population but up to ~28% of severely dyslexic individuals. It is not thought that rs2143340 is a functional SNP; instead, it marks the haplotype known as rs4504469-rs2038137-rs2143340 '1-1-2' since the other two SNPs are the common forms whereas the significant form for rs2143340 is the rare form. The functional effect of this haplotype appears to be on the KIAA0319 gene, in that KIAA0319 gene activity associated with the 1-1-2 risk haplotype is 40% lower than for other haplotype...
14 snps
(hide) Dystonia
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After adjusting for age, sex, and their interaction, a strong association between dystonia and two SNPs, rs13283584 and rs1182 was observed. Intragenic Cis and Trans modification of genetic susceptibility in DYT1 torsion dystonia. [OMIM:TORSIN-A; DYT1]
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After adjusting for age, sex, and their interaction, a strong association between dystonia and two SNPs, rs13283584 and rs1182 was observed. The TOR1A polymorphism rs1182 and the risk of spread in primary blepharospasm. [OMIM:TORSIN-A; DYT1]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Also known as Lys224Arg, G allele is associated with Dopa-Responsive Dystonia. Dystonia with motor delay in compound heterozygotes for GTP-cyclohydrolase I gene mutations. Dopa-responsive dystonia in British patients: new mutations of the GTP-cyclohydrolase I gene and evidence for genetic heterogeneity. Autosomal dominant GTP-CH deficiency presenting as a dopa-responsive myoclonus-dystonia syndrome. [OMIM:?]
3 snps
(hide) Earwax
Magnitude: 2
Frequency: 75.9%
References:12
Frequency: 75.9%
References:12
Wet earwax. Normal body odour. Normal colostrum. This is normal for non-Asians. It makes ear-wax wet, sticky, and honey-coloured. It also produces colostrum for breast feeding. People with this gene need to use deodorant to avoid smelling bad, unlike some Asians.
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rs17822931, also known as c.538G>A or G180R, is a SNP in the ATP-binding cassette, sub-family C (CFTR/MRP), member 11 ABCC11 gene. The ABCC11 protein helps transport small molecules across apical membranes such as those in apocrine secretory cells. This SNP determines wet vs dry earwax as well as sweat production, and it is also associated with lipid secretion. It is commonly (T;T) for Asians and (C;C) for Europeans and Africans. A study of deodorant usage in a large (17,000+) population showed that rs17822931(T;T) individuals were at least 5-fold less likely to use deodorant, consistent with them being 'genotypically nonodorous'. Although not statistically significant, there was some evidence for a heterozygote effect, implying that individuals with a (C;C) genotype for this SNP were l...
1 snp
(hide) Eczema
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http://blog.23andme.com/2012/03/02/snpwatch-new-genetic-insight-into-the-causes-of-eczema/ linked to eczema
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Association study of mast cell chymase polymorphisms with atopy. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. Power of multifactor dimensionality reduction and penalized logistic regression for detecting gene-gene interaction in a case-control study. Impact of polymorphisms of the genes encoding angiotensin II-forming enzymes on the progression of IgA nephropathy.
normal but highest IgE levels
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rs2251746 is a SNP in the gene encoding the alpha chain of the high affinity receptor for IgE (FCER1A) on chromosome 1q23. High levels of serum IgE are associated with allergies, and are mediators of autoimmune diseases. An examination of over 11,000 Germans led to the conclusion that rs2251746 (and one other FCER1A SNP, the tightly linked rs2427837) were strongly associated with high levels of serum IgE. The more common (T) allele was associated with higher serum IgE, and the effect appeared to be additive. Therefore, homozygous rs2251746(C;C) individuals may be at lower risk for atopic eczema and asthma than carriers of one or two (T) alleles. In Japanese patients, rs2251746 may be a poor predictor, and the neighboring rs2427827 may be more appropriate. Common variants in FCER1A influenc...
3 snps
(hide) Ehlers-Danlos syndrome
Mix of muscle types. Likely sprinter. Normal for white people. One working and one defective copy of the gene for alpha-actinin-3 in fast-twitch muscle fibres. This genotype may indicate somewhat impaired muscles, however many sprinters and some endurance athletes have this.
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This SNP, in the ACTN3 gene, encodes a premature stop codon in a muscle protein called alpha-actinin-3. The polymorphism alters position 577 of the alpha-actinin-3 protein. In the (C;C) genotype is often called RR. The truncated (T;T) is often called XX. (T;T) is under-represented in elite strength athletes, consistent with previous reports indicating that alpha-actinin-3 deficiency appears to impair muscle performance. The most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the alternative T allele encodes a stop codon (X). Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. XX individuals completely lack the expression of alpha-actinin-3. An earlier report studying a relatively small number of Austr...
1.33x increased risk of Ulcerative Colitis, but much lower Type 1 Diabetes risk. This raises the risk of Ulcerative Colitis (according to 23andMe), but also greatly lowers the risk of Type 1 Diabetes. It may also affect other autoimmune diseases.
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A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ancestry, concluded that this SNP and several others were associated with altered risk for the disease. [PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 6p21.32; Reported Gene(s): BTNL2, HLA-DRA, HLA-DRB5, HLA-DRB1, HLA-DQA1, HLA-DQB1; Risk Allele: rs2395185-?); (p-value= 0.0000000000000001).This variant is associated with Ulcerative colitis.] [OMIM:?] [GWAS:Ulcerative colitis]
Slightly increased risk of developing restless legs syndrome rs3923809 is a A/G variation on human chromosome 6. Associated with: Restless legs syndrome. This SNP, located in an intron of the BTBD9 gene, has a variant that is seen somewhat more frequently in individuals with restless legs syndrome. The risk allele is rs3923809(A); carriers of two such alleles, i.e. those with rs3923809(A;A) genotypes, are estimated to be 1.9 fold more likely to have restless legs syndrome than rs3923809(G;G) individuals. The authors of this study suggest that perhaps half of the cases of restless legs syndrome may involve the rs3923809 risk genotypes. Consistent with this finding, another report about rs3923809 links the (G) minor allele to a lower frequency of restless legs syndrome with an overall odds ...
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This SNP, located in an intron of the BTBD9 gene, has a variant that is seen somewhat more frequently in individuals with restless legs syndrome. The risk allele is rs3923809(A); carriers of two such alleles, i.e. those with rs3923809(A;A) genotypes, are estimated to be 1.9 fold more likely to have restless legs syndrome than rs3923809(G;G) individuals. The authors of this study suggest that perhaps half of the cases of restless legs syndrome may involve the rs3923809 risk genotypes. Consistent with this finding, another report about rs3923809 links the (G) minor allele to a lower frequency of restless legs syndrome with an overall odds ratio of 0.57 (CI: 0.48-0.68). Note that 70-80% of all individuals in European populations carry one or two copies of the (A) major allele, yet restless le...
1.1x risk Crohn's Disease
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rs9858542 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.09 (CI 0.96-1.24), and for homozygotes, 1.84 (CI 1.49-2.26). [PharmGKB:Non-Curated GWAS results: Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: 1,182 cases, 2,024 controls). This variant is associated with Crohn's disease.] [OMIM:INFLAMMATORY BOWEL DISEASE 12; IBD12] [GWAS:Ulcerative colitis] [GWAS:Crohn's disease]
0.94 reduced risk of cleft lip / palate We found a reduced risk of CL/P with mothers who carried the CBS C699T variant (rs234706); relative risk was 0.94 with one copy of the T allele (95% CI 0.63-1.4) and 0.50 (95% CI 0.26-0.96) with two copies (P = 0.008). PMID: 18203168
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Being investigated in Ehlers-Danlos syndrome
CYP2C9*2 carrier; average 20% reduction in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene and is linked to poor warfarin metabolism. Advanced knowledge of this may influence initial warfarin dosing by physicians. Warfarin is monitored through INR (international normalized ratio) and proper dosing is influenced by a variety of factors including warfarin metabolism and diet. rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The CYP2C9*2 allele is also associated with higher sensitivity to the anti-epileptic drug phenytoin. The effect of CYP2C9 variants on drug metabolism should not be pr...
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Nearsightedness and Farsightedness
Normal 0.97x risk for Age Related Macular Degeneration. When the retina cells in the eye get damaged with age, it is known as Age Related Macular Degeneration. This SNP has about the average risk. The SENS Research Foundation is working on a promising cure for Age Related Macular Degeneration: http://www.sens.org/outreach/conferences/lysosens-synthetic-biology-approach-treat-age-related-macular-degeneration
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may influence age related macular degeneration (damage to the eye with ageing) when part of the haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC), but does not appear to do so alone. age related macular degeneration [GWAS:Age-related macular degeneration]
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Being investigated in Ehlers-Danlos syndrome
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
normal
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Several SNPs in the VKORC1 gene have been linked to warfarin sensitivity, with perhaps the most common being this SNP rs9923231. Note that the orientation as published in scientific articles is often on the opposite strand compared to the orientation in dbSNP, so you will sometimes see it as a G>T snp. It is also known as *-1639G>A with the minus indicating that this is in an upstream promoter *3673 based on its position in GenBank accession number AY587020. *VKORC1*2. The main findings related to the treatment of venous thromboembolism (aka VTE; from hypercoagulability) with the blood thinner warfarin for this SNP are that carriers of the rs9923231(T) allele require significantly reduced doses of warfarin, and are (otherwise) at a higher risk of serious bleeding. Clinical studies de...
normal
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rs2274223 is a SNP in the phospholipase C, epsilon 1 PLCE1 gene. In a large study of Han Chinese esophageal cancer patients [specifically esophageal squamous cell carcinoma (ESCC)], the rs2274223(G) allele was associated with greater risk (odds ratio 1.43, p = 7.4 x 10e-56).In this same study [http://www.nature.com/ng/journal/vaop/ncurrent/ris/ng.648.ris, rs2274223(G) was also associated with greater risk for gastric cancer (aka stomach cancer), with an odds ratio of 1.55 (1.74 x 10e-39). [OMIM:?] [GWAS:None]
normal
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rs1800255 is a SNP in the alpha I chain of the type III collagen protein-encoding COL3A1 gene. A relatively small study (200 patients) reported an odds ratio of 5 (CI: 1.4-17.1) between rs1800255(A;A) homozygotes and risk for pelvic organ prolapse. No significance was found for the heterozygous genotype. [OMIM:?]
Magnitude: 0
Frequency: 78.5%
Repute:Good
References:5
Frequency: 78.5%
Repute:Good
References:5
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[OMIM:LAMININ, GAMMA-1; LAMC1]
common in complete genomics
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rs547154 significantly associated with Age-related maculopathy in both our case-control (P-value 0.00007) and family data (P-value 0.00001). [OMIM:COMPLEMENT COMPONENT 2 DEFICIENCY]
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
Typical BuChE
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rs1799807, also known as D70G, is a SNP in the BCHE gene. This SNP affects the structure, activity, and substrate specificity of the BuChE (butyrylcholinesterase) enzyme. [Cholinesterases and cholinesterase inhibitors, p. 48] The variant form, rs1799807(G), replaces aspartate with glycine at the secondary substrate/inhibitor binding site. This single base substitution yields the 'atypical' version of BChE. This version has a lower affinity for many substrates, including many Cholinesterase Inhibitors (CIs). A different cholinesterase (acetylcholinesterase, AChE) is an important component of neurotransmission by acetylcholine (ACh), terminating the action of ACh after it has been released during neurotransmission. BChE is found widely in the plasma and normally binds to CIs, protecting AChE...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
24 snps
(hide) Emphysema
1.75-fold reduced risk of developing lung cancer The frequency of the minor allele A of '''rs31489''' was 32.49% in cancer patients versus 45.79% in disease-free subjects. Subjects carrying one copy of minor allele A are at 1.75-fold reduced risk of developing lung cancer.
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[GWAS:Lung adenocarcinoma]
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rs1051740, also known as Tyr113His, is a SNP in the microsomal epoxide hydrolase EPHX1 gene. severe hypersensitivity syndrome, triggered by carbamazepine in the presence of a concomitant active human herpes virus (HHV) 6 and 7 infection with the allele HLA-A*3101 and rs1051740(C;C) [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a logistic regression model adjusted for history of phenytoin use during the first trimester and maternal epilepsy, the maternal EPHX1 113 H (rs1051740 T/C) allele was associated with craniofacial abnormalities in the child. Study size: 157 pregnancies. Study population/ethnicity: phenytoin use during the first trimester and maternal epilepsy. metric(s): per rare allele OR: 2.43, 95% confidence interval (CI): 1.16-5.10, P=0.02. Type of asso...
normal
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rs975278 is a SNP in the SERPINE2 gene. A study involving 1,335 consecutive autopsies of elderly Japanese people found emphysema of more than moderate degree in 189 subjects and among 12 examined SNPs, found that only rs975278 was positively associated (with emphysema).rs975278(A;A) individuals were associated with emphysema (odds ratio 1.54, CI: 1.02-2.30, p = 0.037) and the association was more prominent in smokers (odds ratio 2.02, CI: 1.29-3.15, p = 0.002).
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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rs28931569 is a SNP representing an amino acid change in the SERPINA1 gene, which encodes alpha-1-antitrypsin (AAT). Carriers of two rs28931569(C) alleles, i.e. homozygotes, are at high risk for emphysema . [OMIM:PI M(PROCIDA)]
common in complete genomics
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rs17580, also known as the S or PiS allele, is a SNP in the SERPINA1 gene. Levels of alpha-1 antitrypsin (encoded by the SERPINA1 gene) may be reduced in carriers of the rs17580(T) allele, but there is no known association with liver disease or cystic fibrosis. The rs17580 PiS variant is most associated with risk of developing COPD, especially in smokers, but it's association with emphysema is variable. See rs28929474 for the most common pathologic SNP (PiZ) in the SERPINA1 gene. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is T, but test results may be in the plus orientation where the risk allele is A (although currently 23andMe reports the risk allele as T). This SNP has an ambiguous flip which can make...
5 snps
(hide) Endometrial cancer
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
Women have lower risk of Endometriosis but normal risk for Endometrial Cancer, and more cognitive impairment with age. Men have zero risk, but can pass this on to their daughters. This is the normal version of Estrogen Receptor 1 (alpha). It has more cognitive decline than the rare version, with old women only remembering half as much details on the East Boston Memory Test immediate recall test.
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rs9340799 is a SNP in the estrogen alpha receptor ESR1 gene, and it is also known as the -351A>G variant. Among women, rs8179176, rs9340799, rs1256065, and rs1256030 were associated with likelihood of developing cognitive impairment with ageing. In men, rs728524, rs1255998, and rs1256030 were associated with cognitive impairment. A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs9340799) and risk of ischemic stroke. A study of 702 cases with invasive endometrial cancer concluded that the less common alleles of SNP rs9340799 lowered risk for the disease. The odds ratio was 0.75 (CI: 0.60-0.93) for (A;G) and 0.53 (CI: 0.37-0.77) for (G;G) compared to rs9340799(A;A) individuals. Endometriosis Uterine Fibroids [PharmGKB:Curated SNP i...
1.3x higher risk for endometrial cancer (in Chinese women)
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Category:interestingrs34330 shows an association with breast cancer in a British study involving ~2300 patients. The odds ratio for the (T;T) vs (C;C) homozygotes is 1.22 (CI: 1.02-1.47, p=0.013). found a significant association between rs34330 (-79C/T) and prostate cancer found higher odds for endometrial cancer among 1,200+ Chinese patients associated with rs34330, with an odds ratio of 1.33 (CI: 1.06-1.66) and 1.51 (CI: 1.16-1.94) for the (C;T) and (T;T) genotypes, respectively, compared with the (C;C) genotype. see also omim 176807 [OMIM:CYCLIN-DEPENDENT KINASE INHIBITOR 1B; CDKN1B] [GWAS:Systemic lupus erythematosus]
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Part of a haplotype Gs286, standalone effect for endometrial cancer is ambiguous. In , no evidence for linkage to colorectal cancer in women was found in a study with 158 European subjects and 563 controls. Genetic variation in sex-steroid receptors and synthesizing enzymes and colorectal cancer risk in women. Catalog of 668 SNPs detected among 31 genes encoding potential drug targets on the cell surface An Epidemiologic Study of Genetic Variation in Hormonal Pathways in Relation to the Effect of Hormone Replacement Therapy on Breast Cancer Risk [GWAS:Endometrial cancer]
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[GWAS:Endometrial cancer]
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* rs2279744, rs1042522, rs17878362 and rs1625895 associated with high grade endometrial cancer
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Part of a haplotype Gs286, standalone effect for endometrial cancer is ambiguous. No statistically significant interaction with 17-alpha-hydroxyprogesterone caproate for reducing recurrent preterm birth detected. Progesterone receptor polymorphisms and clinical response to 17-alpha-hydroxyprogesterone caproate Clarifying the PROGINS allele association in ovarian and breast cancer risk: a haplotype-based analysis [GWAS:Endometrial cancer]
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[GWAS:Endometrial cancer]
Frequency: 36.3%
References:1
References:1
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[GWAS:Endometrial cancer]
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endometrial cancer rs727479(A) odds ratio per allele of 1.08, 95% confidence interval of 1.02-1.14, and P = 0.009 Association analyses of CYP19 gene polymorphisms with height variation in a large sample of Caucasian nuclear families. Polymorphisms of estrogen-biosynthesis genes CYP17 and CYP19 may influence age at menarche: a genetic association study in Caucasian females. Genetic variation at the CYP19A1 locus predicts circulating estrogen levels but not breast cancer risk in postmenopausal women. Haplotype analyses of CYP19A1 gene variants and breast cancer risk: results from the Shanghai Breast Cancer Study. A single-nucleotide polymorphism in the aromatase gene is associated with the efficacy of the aromatase inhibitor letrozole in advanced breast carcinoma. Association of genetic poly...
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rs749292(A) associated with ovarian cancer risk in a codominant model for all races combined [AG versus AA genotype: odds ratio (OR), 1.48 and 95% confidence interval (CI), 1.07-2.04); GG versus AA: OR, 1.87 (CI, 1.24-2.82); Ptrend =0.002]. endometrial cancer *rs749292(A) allele OR of 1.14, 95% confidence interval of 1.09-1.21, and P = 7.1 x 10(-7) *rs727479(A) odds ratio per allele of 1.08, 95% confidence interval of 1.02-1.14, and P = 0.009 [OMIM:CYTOCHROME P450, FAMILY 19, SUBFAMILY A, POLYPEPTIDE 1; CYP19A1]
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Part of a haplotype Gs286, standalone effect for endometrial cancer is ambiguous. Clarifying the PROGINS allele association in ovarian and breast cancer risk: a haplotype-based analysis [GWAS:Endometrial cancer]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
Frequency: 51.3%
References:1
References:1
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[GWAS:Endometrial cancer]
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Part of a haplotype Gs286, standalone effect for endometrial cancer is ambiguous. Tightly linked with PROGINS allele. Clarifying the PROGINS allele association in ovarian and breast cancer risk: a haplotype-based analysis [GWAS:Endometrial cancer]
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Part of a haplotype Gs286, standalone effect for endometrial cancer is ambiguous. Clarifying the PROGINS allele association in ovarian and breast cancer risk: a haplotype-based analysis [GWAS:Endometrial cancer]
References:17
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* rs2279744, rs1042522, rs17878362 and rs1625895 associated with high grade endometrial cancer
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Part of a haplotype Gs286, standalone effect for endometrial cancer and ovarian cancer is ambiguous. ''p''-values account for ethnic heterogenity of study population. Clarifying the PROGINS allele association in ovarian and breast cancer risk: a haplotype-based analysis [GWAS:Endometrial cancer]
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Part of a haplotype Gs286, standalone effect for endometrial cancer is ambiguous. ''p''-values account for ethnic heterogenity of study population. In , no evidence for linkage to colorectal cancer in women was found in a study with 158 European subjects and 563 controls. Genetic variation in sex-steroid receptors and synthesizing enzymes and colorectal cancer risk in women. [GWAS:Endometrial cancer]
normal risk
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Minor allele (T) of this SNP uniquely identifies what is known as the PROGINS allele in the progresterone receptor gene PGR. Two SNP's tagging a partial haplotype of the PGR gene were associated with an increased risk of ovarian cancer among homozygous carriers as compared with noncarriers: rs1042838 (PROGINS allele; odds ratio [OR] = 3.23, 95% confidence interval [CI] = 1.19 to 8.75, P = .022) and rs608995 (minor allele; OR = 3.10, 95% CI = 1.63 to 5.89, P<.001). The study suggest the effect is likely entirely due to rs608995, whose minor allele was almost always seen with PROGINS allele. For rs1042838, the risk allele in orientation to the corresponding dbSNP entry is (T). Subsequent studies have not replicated this high odds ratio, nor the apparent recessive model in this study. The ...
normal
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rs2279744, a variant in the promoter of the MDM2 gene and also known as '-410T-G', 'SNP309', and 'SNP309T>G', has been studied for several years to determine it's role in cancer origin and treatment. The interest primarily stems from the ability of the MDM2 protein to bind to and thereby enhance the degradation of the tumor suppressor protein known as p53. Studies on rs2279744 include: * rs2279744(G) carriers in individuals with cancer tend to develop such cancers on average 12 years earlier than those lacking this allele, and the frequency of rs2279744(G) was greatly increased in those who developed soft tissue sarcomas at a young age. * Individuals with one or more rs2279744(G) alleles who are also carriers of the TP53 rs1042522(C) (arg at aa72) SNP tend to develop cancers earlier tha...
22 snps
(hide) Endometriosis
Women have lower risk of Endometriosis but normal risk for Endometrial Cancer, and more cognitive impairment with age. Men have zero risk, but can pass this on to their daughters. This is the normal version of Estrogen Receptor 1 (alpha). It has more cognitive decline than the rare version, with old women only remembering half as much details on the East Boston Memory Test immediate recall test.
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rs9340799 is a SNP in the estrogen alpha receptor ESR1 gene, and it is also known as the -351A>G variant. Among women, rs8179176, rs9340799, rs1256065, and rs1256030 were associated with likelihood of developing cognitive impairment with ageing. In men, rs728524, rs1255998, and rs1256030 were associated with cognitive impairment. A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs9340799) and risk of ischemic stroke. A study of 702 cases with invasive endometrial cancer concluded that the less common alleles of SNP rs9340799 lowered risk for the disease. The odds ratio was 0.75 (CI: 0.60-0.93) for (A;G) and 0.53 (CI: 0.37-0.77) for (G;G) compared to rs9340799(A;A) individuals. Endometriosis Uterine Fibroids [PharmGKB:Curated SNP i...
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
Magnitude: 1.5
Frequency: 40.7%
Repute:Bad
References:2
Frequency: 40.7%
Repute:Bad
References:2
Slight (~1.2x) increase in endometriosis risk
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==='''Summary of trait'''=== Endometriosis is a disorder in which the endometrium, which lines the inside of a woman’s uterus grows outside the uterus (etopic). It affects 6% - 10% of women of reproductive age. In a patient with endometriosis, the endometrial tissue behaves normally, whereby during a menstrual cycle, it would thicken, break down and bleed out. Being outside the uterus, the broken down endometrial tissue cannot leave the body. This blood will irritate surrounding tissue, causing scar tissue and adhesions and may potentially bind organs together. Endometriosis may involve ovaries, bowel or tissue lining pelvis. Cysts (or endometriomas) may form if endometriosis involves ovaries . The exact cause of endometriosis is unknown, but the most widely accepted theory is the retrogra...
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[GWAS:Endometriosis]
Frequency: 25.7%
References:1
References:1
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[GWAS:Endometriosis]
Frequency: 47.8%
References:2
References:2
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[GWAS:Endometriosis]
0.5x decreased risk for endometriosis
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rs1800871(C) carriers are associated with a reduced endometriosis risk by approximately 2x compared with the common rs1800871(T;T) genotype in a study of 196 Chinese patients. rs2222202 (C/T) (p=0.03) and rs1800871 (C/T) (p=0.05) showed significant allelic associations with pediatric onset Crohn's disease. rs1800871(T) carriers were 3x more likely to have their pregnancies terminate early (<10 weeks) than (C) carriers, based on a study of ~500 pregnancies. In a study of 1,757 cases of Alzheimer's disease and 6,295 controls, an interaction was replicated between IL6 genotype rs2069837(A;A) and IL10 genotype rs1800871(C;C). The synergy factor (SF) was 1.63 (CI: 1.10-2.41, p = 0.01), controlling for age, gender and ApoE4 genotype. 23andMe reports that each G allele at rs1800871 is associat...
Magnitude: 0
Frequency: 92.8%
Repute:Good
References:1
Frequency: 92.8%
Repute:Good
References:1
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[GWAS:Endometriosis]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
10 snps
(hide) Eosinophilic esophagitis
normal Eosinophilic esophagitis (EE) is an emerging worldwide disease, as documented by recent case series from Switzerland, Australia, Canada, Japan, England, and the US (1–4). Of concern, EE appears to be a growing health problem with an annual incidence of at least 1 in 10,000 children (5). The primary symptoms of EE (chest and abdominal pain, dysphagia, heartburn, vomiting, and food impaction) are also observed in patients with chronic esophagitis (CE) including gastroesophageal reflux disease (GERD) (6–8). However, in contrast to GERD, EE occurs more frequently in males (80%), appears to have a common familial form, has a high rate of associated atopic disease (70%), and is typically associated with a normal pH probe recording of the esophagus (5, 9, 10) In the 3? untrans...
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rs2302009 is a SNP located in the 3' untranslated region of the CCL26 gene. This gene (and this SNP) were discovered to be strongly associated with 117 patients with eosinophilic esophagitis, a form of esophagitis (or inflammation of the esophagus) that shares many symptoms with gastroesophageal reflux disease (GERD). rs2302009(G) is the risk allele. The rs2302009(G;G) homozygous genotype is the most predisposed to developing eosinophilic esophagitis (odds ratio 4.55, CI 1.71–12.39). The heterozgyote (rs2302009(G;T)) genotype's risk was indistinguishable statistically from the normal rs23020099(T;T) genotype. [OMIM:ESOPHAGITIS, EOSINOPHILIC]
1 snp
(hide) Epilepsy
Frequency: 14.1%
References:1
References:1
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rs11031434 is a SNP in the elongator protein complex 4 ELP4 gene. * Associated with rolandic epilepsy, as part of a relatively tightly linked cluster of 3 SNPs (rs964112, rs11031434, and rs986527. Centrotemporal sharp wave EEG trait in rolandic epilepsy maps to Elongator Protein Complex 4 (ELP4). [OMIM:?]
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May Underlie Susceptibility to Adolescent-Onset Idiopathic Generalized Epilepsy] [OMIM:MALIC ENZYME 2; ME2]
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rs964112 is a SNP in the elongator protein complex 4 ELP4 gene. * Associated with rolandic epilepsy, as part of a relatively tightly linked cluster of 3 SNPs (rs964112, rs11031434, and rs986527. [OMIM:?]
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
normal/common
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rs2273697, also known as c1249G>A or p.V471I, is a nonsynonymous polymorphism in the ABCC2 gene. From an initial case-control study of 146 patients with epilepsy, followed by replication (p=0.001) in another 279 patients, the rs2273697(A) allele was associated with neurological adverse drug reactions from taking carbamazepine. Functional studies showed that this SNP selectively reduced carbamazepine transport across the cell membrane. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP showed a strong association with the neurological adverse drug reaction caused (ADR) by carbamazepine (P=0.005). The study results indicate that the c.1249A variant is an independent risk factor of carbamazepine CNS ADR. Study size: 146 patients with epilepsy who had been prescr...
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[OMIM:GAMMA-AMINOBUTYRIC ACID RECEPTOR, BETA-3; GABRB3]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
11 snps
(hide) Erythropoietic protoporphyria
common in clinvar
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rs2272783, also known as IVS3-48T-C, is a mutation in the ferrochelatase FECH gene leading to lowered expression of that enzyme. When coupled in trans with a nonfunctional FECH allele, this is likely to lead to Erythropoietic protoporphyria. See also: OMIM 612386.0015
2 snps
(hide) Factor XI deficiency
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs121965063, also known as E117X or Glu117Ter, is a SNP in the coagulation factor XI F11 gene. This SNP is reported by 23andMe as one of the three most common factor XI deficiency-causing mutations in Ashkenazi Jews; it is reported as i4000398 by 23andMe. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs121965064, also known as F283L or Phe283Leu, is a SNP in the coagulation factor XI F11 gene. This SNP is reported as one of the three most common factor XI-deficiency causing mutations in Ashkenazi Jews; it is reported as i4000399 by 23andMe. [OMIM:?]
5 snps
(hide) Familial dysautonomia
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs111033171, also known as IVS20_6T>C, is a SNP in the inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein IKBKAP gene. This is reported as one of two mutations accounting for 99% of the cases of familial dysautonomia in Ashkenazi Jews; in 23andMe, it is reported as i4000334. Be aware of strand flipping issues in how this SNP is reported. [OMIM:?]
1 snp
(hide) Familial hypercholesterolemia
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Familial hypercholesterolemia; aka FH Lithuania, the most common FH mutation in Ashkenazi Jews see rs121908027
common in complete genomics
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rs505151 is a SNP, also known as E670G or 23968A>G, in the proprotein convertase subtilisin/kexin type 9 PCSK9 gene. rs505151(G) encodes the Gly (G), and rs505151(A) encodes the Glutamic acid (E). In a study of 506 European polygenic hypercholesterolemia patients, the rs505151(G) allele was found with increased frequency in men but not in women. rs505151 rs562556 show evidence of 'gain-of-function' mutations that are associated with higher LDL cholesterol levels. Longitudinal association of PCSK9 sequence variations with low-density lipoprotein cholesterol levels: the Coronary Artery Risk Development in Young Adults Study. The proprotein convertase subtilisin/kexin type 9 gene E670G polymorphism and serum lipid levels in the Guangxi Bai Ku Yao and Han populations. Genetic variability wi...
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in clinvar
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rs12713559, also known as R3531C, is a SNP in the APOB apolipoprotein B gene. The risk allele is A according to 23andMe, which tests for this SNP in regard to familial hypercholesterolemia type B, and where they note that the evidence is unclear about whether this mutation is causative on its own. In SNPedia, where we use the orientation as defined by dbSNP, the risk allele is rs12713559(T). Familial Hypercholesterolemia Type B [OMIM:?]
normal
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rs5742904, also known as R3527Q or R3500Q, is a SNP in the APOB apolipoprotein B gene. The risk allele is T according to 23andMe, which tests for this SNP in regard to familial hypercholesterolemia type B. In SNPedia, where we use the orientation as defined by dbSNP, the risk allele is rs5742904(A). For a clinical case discussion of this SNP, see 'Clinical Case 2' within Box 1 of . Familial Hypercholesterolemia Type B [OMIM:HYPERCHOLESTEROLEMIA DUE TO LIGAND-DEFECTIVE APOLIPOPROTEIN B100]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common/normal
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rs144467873, also known as R3500W, is a SNP in the APOB apolipoprotein B gene. The risk allele is A according to 23andMe, which tests for this SNP in regard to familial hypercholesterolemia type B under the name i4000339. This SNP is found mainly in Asian populations.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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(A;A) familial hypercholesterolemia 23% frequency among Afrikaners 1.5% frequency among Dutch [OMIM:FH AFRIKANER 2]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
8 snps
(hide) Familial hypertrophic cardiomyopathy
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rs397516074 familial hypertrophic cardiomyopathy
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see discussion at rs397515963 familial hypertrophic cardiomyopathy
common in clinvar
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Familial hypertrophic cardiomyopathy see also OMIM 160760.0002 [OMIM:CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 1]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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Familial hypertrophic cardiomyopathy see also OMIM 188840.0001 [OMIM:CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 9]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Familial hypertrophic cardiomyopathy see also OMIM 602743.0004 [OMIM:CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, WITH WOLFF-PARKINSON-WHITE SYNDROME]
5 snps
(hide) Familial Mediterranean Fever
Magnitude: 0
Frequency: 98.4%
Repute:Good
References:7
Frequency: 98.4%
Repute:Good
References:7
common in clinvar
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rs11466023, also known as P369S, is a SNP in the MEFV gene. The risk allele is given as (A) by 23andMe, however in dbSNP orientation, the risk allele is (T). The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. [OMIM:FAMILIAL MEDITERRANEAN FEVER]
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Familial Mediterranean Fever rs104895083
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possibly Familial Mediterranean Fever but causation is not proven rs104895094
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Familial Mediterranean Fever rs61732874
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Familial Mediterranean Fever rs104895097
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs104895097, also known as R761H, is a SNP in the MEFV gene. The equivalent SNP for 23andMe is i4000410. The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs28940578, also known as M694I, is a SNP in the MEFV gene. The risk allele is given as (T) by 23andMe, however in dbSNP orientation, the risk allele is (A). The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. Genetic variation in the familial Mediterranean fever gene (MEFV) and risk for Crohn's disease and ulcerative colitis. A rapid accurate assay for choline kinase. Mutation and haplotype studies of familial Mediterranean fever reveal new ancestral relationships and evidence for a high carrier frequency with reduced penetrance in the Ashkenazi Jewish population. MEFV-Gene analysis in armenian patients with Fam...
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
common in clinvar
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rs28940579, also known as V726A, is a SNP in the MEFV gene. The risk allele is given as (G) by 23andMe, however in dbSNP orientation, the risk allele is (C). The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. [OMIM:FAMILIAL MEDITERRANEAN FEVER]
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
common in clinvar
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rs28940580, also known as M680I, is a SNP in the MEFV gene. The risk allele is given as (G) by 23andMe, however in dbSNP orientation, the risk allele is (C). The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. [OMIM:FAMILIAL MEDITERRANEAN FEVER]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
common in clinvar
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rs61732874, also known as A744S, is a SNP in the MEFV gene. The equivalent SNP for 23andMe is i4000409. The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. [OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
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rs61752717, also known as M694V, is a SNP in the MEFV gene. [OMIM:?]
common in clinvar
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rs104895083, also known as F479L, is a SNP in the MEFV gene. The equivalent SNP for 23andMe is i4000403. The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. Non-founder mutations in the MEFV gene establish this gene as the cause of familial Mediterranean fever (FMF). [OMIM:?]
common in clinvar
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rs3743930, also known as E148Q, is a SNP in the MEFV gene. The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. Genetic variation in the familial Mediterranean fever gene (MEFV) and risk for Crohn's disease and ulcerative colitis. Missense mutations in the MEFV gene are associated with fibromyalgia syndrome and correlate with elevated IL-1beta plasma levels. On the latency and form of the membrane responses of smooth muscle to the iontophoretic application of acetylcholine or carbachol. MEFV mutations in Behcet's disease. The differential contribution of MEFV mutant alleles to the clinical profile of familial Medi...
14 snps
(hide) Fanconi anemia
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Fanconi Anemia rs104886459
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs104886457, also known as R548* or R548X, is a SNP in the Fanconi anemia, complementation group C FANCC gene. 23andMe reports that this causative mutation for Fanconi anemia is found mainly in non-Jewish people with European ancestry. The term 23andMe uses for this SNP is i4000412. [OMIM:?]
common in complete genomics
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rs104886456, also known as IVS4+4A>T, is a SNP in the Fanconi anemia, complementation group C FANCC gene. 23andMe reports that this mutation is carried by approximately 1% of Ashkenazi Jews and is responsible for more than 99% of FANCC-related Fanconi anemia in this population. This same mutation is the most common cause of FANCC-related Fanconi anemia in Japan. The term 23andMe uses for this SNP is i4000336. [OMIM:?]
6 snps
(hide) Fetal alcohol syndrome
common one paper reports increased risk of alcoholism for African-Americans with this genotype.
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This paper found significant association with rs2066702, the SNP that defines ADH1B*3, in African American families. Association was strongest with the ICD-10 definitions of alcoholism, with P=0.046 for PDTsum and 0.029 for PDTaverage; it was also significant for DSM-IV for PDTaverage (P=0.039). The high-risk allele was the C that encodes ADH1B*1, and the low-risk allele encodes ADH1B*3. A review of the (at times conflicting) findings regarding ADH1B genotypes and maternal and fetal alcohol syndromes is available.In some African American] and Native American populations, the ADH1B*3 allele (Arg369Cys in exon 9) is correlated with protection against alcoholism. [PharmGKB:In-Depth This allele has been found in some African American and Native American populations to be correlated with prote...
1 snp
(hide) Fibromyalgia
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
normal
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
normal
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rs4994, also known as Trp64Arg or as the Arg64 variant, is a SNP in the ADRB3 gene. The rs4994(C) allele encodes the variant arginine. In a study of 600+ women initially referred for coronary angiography and then followed for 6 years, during which time 115 experienced a heart problem, rs4994(C) individuals were calculated to be at higher risk (adjusted hazard ratio 2.10, CI: 1.05-4.24). This risk was due to subtle increases in risk for all of the individual endpoints, and was only seen in women without obstructive coronary artery disease. Response to Diet and Exercise [PharmGKB:Curated Arg in position 64 associated with olanzapine-induced weight gain] [OMIM:OBESITY, SUSCEPTIBILITY TO]
7 snps
(hide) Focal segmental glomerulosclerosis
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Focal segmental glomerulosclerosis 2 rs121434391
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Focal segmental glomerulosclerosis 2 rs121434392
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Focal segmental glomerulosclerosis 2 rs121434394
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Focal segmental glomerulosclerosis 1 rs121908415
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Focal segmental glomerulosclerosis 1 rs121908416
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Focal segmental glomerulosclerosis 1 rs121908417
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Focal segmental glomerulosclerosis 2 rs121434390
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Focal segmental glomerulosclerosis 2 rs121434395
8 snps
(hide) Food allergy
3x increased risk for developing a peanut allergy In populations of European ancestry, having two copies of a rs9275596(C) allele is associated with 3x increased risk for developing a peanut allergy.
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rs9275596 is a SNP located between the HLA-DQB1 and HLA-DQA2 genes on chromosome 6. A study of several thousand children and their parents, most with food allergies, concluded that two SNPs, rs7192 and rs9275596, are associated with increased susceptibility to developing a peanut allergy in populations of European ancestry. The odds ratio reported for rs9275596(C) were 1.7 (p=10e-10). Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. A two-stage search strategy for detecting multiple loci associated with rheumatoid arthritis. Kidney Disease [GWAS:None]
1.7x increased risk for developing a peanut allergy In populations of European ancestry, the rs7192(T) allele is associated with somewhat increased risk for developing peanut allergies.
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rs7192, also known as Leu242Val or L242V, is a SNP in the HLA-DRA gene on chromosome 6. A study of several thousand children and their parents, most with food allergies, concluded that two SNPs, rs7192 and rs9275596, are associated with increased susceptibility to developing a peanut allergy in populations of European ancestry. The odds ratio reported for rs7192(T) were 1.7 (p=10e-8). Detecting significant single-nucleotide polymorphisms in a rheumatoid arthritis study using random forests [OMIM:?] [GWAS:None]
2 snps
(hide) Frontotemporal dementia
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Characteristics of frontotemporal dementia patients with a Progranulin mutation. Progranulin mutations in primary progressive aphasia: the PPA1 and PPA3 families. Clinicopathologic correlation in PGRN mutations. Phenotypic variability associated with progranulin haploinsufficiency in patients with the common 1477C-->T (Arg493X) mutation: an international initiative. Distinct genetic forms of frontotemporal dementia. [OMIM:?]
15 snps
(hide) Fuchs' dystrophy
common in complete genomics
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rs613872 is an intronic SNP in the transcription factor 4 TCF4 gene on ch18q21.2. This GWAS study reported in 2010 the association between several independent TCF4 SNPs and Fuchs' dystrophy, including rs613872. They estimated the population attributable risk at about 60% for the rs613872 risk genotypes; in other words, barring other interactions, the relatively common minor allele rs613872(G) is associated with over half of all reported cases of Fuchs' dystrophy in the patient group studied. That does not mean it is causative, though; after all, ~30% of the CEU population carries this allele but the fraction developing Fuchs' dystrophy is less than 5%, so most rs613872(G) carriers are not diagnosed with the disorder. rs613872 was found to be associated with Fuchs' dystrophy based on a stud...
common
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rs9954153 is a SNP in the transcription factor 4 TCF4 gene. It is one of several TCF4 SNPs reported to be independently associated with Fuchs' dystrophy.
2 snps
(hide) Gallbladder cancer
3.5x risk of hep-cancer in cirrhosis patients; higher glioma risk; 3x higher gallbladder cancer risk in females
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rs4444903 is a SNP, also known as +61, located in the promoter region of the epidermal growth factor EGF gene that influences the amount of EGF produced. The rs4444903(G) allele appears to produce higher amounts of EGF than the (A) allele. A study of 2 Caucasian populations of patients with alcoholic cirrhosis indicates that, for these patients, the presence of the risk allele rs4444903(G) increases the chances of developing hepatocellular carcinoma (liver cancer). After adjusting for age, sex, race, etiology, and severity of cirrhosis the number of (G) copies led to an odds ratio for either (G;G) or (A;G) genotypes versus the (A;A) genotype of 3.49 (CI: 1.29-9.44, p=.01). In another study, analysis of 197 glioma patients showed that the rs4444903(G) allele conferred higher risks for gliom...
increased risk in men for biliary conditions
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rs440446 is a SNP in an intron of the apolipoprotein E APOE gene; it is also known as the IVS1+69 variant. In a study of ~1,000 Chinese patients with various biliary tract conditions, including cancer and gallstones, men carrying a rs440446(C) allele (in dbSNP orientation) had a 1.7x risk of gallstone disease [CI: 1.2-2.4], a 1.8x risk of gallbladder cancer (CI: 1.0-3.3), a 3.7x risk of bile duct cancer (CI: 2.0-7.0), and a 4x risk of ampullary cancer (CI: 1.4-12.4). Note: orientation relative to dbSNP entry is reversed as published. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. Subarachnoid hemorrh...
2 snps
(hide) Gallstone disease
normal
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rs4994, also known as Trp64Arg or as the Arg64 variant, is a SNP in the ADRB3 gene. The rs4994(C) allele encodes the variant arginine. In a study of 600+ women initially referred for coronary angiography and then followed for 6 years, during which time 115 experienced a heart problem, rs4994(C) individuals were calculated to be at higher risk (adjusted hazard ratio 2.10, CI: 1.05-4.24). This risk was due to subtle increases in risk for all of the individual endpoints, and was only seen in women without obstructive coronary artery disease. Response to Diet and Exercise [PharmGKB:Curated Arg in position 64 associated with olanzapine-induced weight gain] [OMIM:OBESITY, SUSCEPTIBILITY TO]
common in complete genomics
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rs3758650 is a SNP in the cadherin-related family member 5 CDHR5 gene. A study of 452 Taiwanese patients with gallstone disease found association between rs3758650 and risk for this disorder, with an odds ratio of 1.59 (adjusted p=0.013) for the rs3758650(A;G) genotype and 5.82 (adjusted p=0.007) for the rs3758650(A;A) genotype when compared with the reference (G;G) genotype.
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:3
Frequency: 85.0%
Repute:Good
References:3
common in complete genomics
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rs41360247 increases susceptibility to Gallstone disease 2.30 times for carriers of the C allele
common in complete genomics
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The 23andMe blog reports that the minor allele of this SNP (A) is associated with decreased LDL levels, increased HDL cholesterol levels, and decreased triglyceride levels. DeCode reports that the G allele is associated with a lower risk of gallstone disease (cholelithiasis) . {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 ...
normal risk for gallstones
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rs11887534, a SNP in the hepatic cholesterol transporter ABCG8 gene, has been implicated in gallstone disease, a process known formally as cholelithiasis. The common allele, rs11887534(G), encodes the aspartic acid (D), while the minor (C) allele encodes histidine (H). In a study of ~1,000 German patients, the overall odds ratio associated with rs11887534(C) carriers was 2.2 (CI: 1.8-2.6, p=1.4x10<sup>-14</sup>), and for (C;C) homozygotes, 7x. Up to 10% of the population attributable risk for gallstones may be accounted for by this SNP. [PharmGKB:Curated GWAS Results: A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease (Initial Sample Size: 280 cases, 360 controls; Replication Sample Size: 2...
increased risk in men for biliary conditions
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rs440446 is a SNP in an intron of the apolipoprotein E APOE gene; it is also known as the IVS1+69 variant. In a study of ~1,000 Chinese patients with various biliary tract conditions, including cancer and gallstones, men carrying a rs440446(C) allele (in dbSNP orientation) had a 1.7x risk of gallstone disease [CI: 1.2-2.4], a 1.8x risk of gallbladder cancer (CI: 1.0-3.3), a 3.7x risk of bile duct cancer (CI: 2.0-7.0), and a 4x risk of ampullary cancer (CI: 1.4-12.4). Note: orientation relative to dbSNP entry is reversed as published. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. Subarachnoid hemorrh...
6 snps
(hide) Gastric cancer
increased risk of gastric and bladder cancer
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rs2976392 and diffuse-type gastric cancer (allele-specific odds ratio (OR) = 1.62, 95% CI = 1.38-1.89, P = 1.11 x 10(-9)). Substitution of the C allele with the risk allele T at a SNP in the first exon (rs2294008, which has r(2) = 0.995, D' = 0.999 with rs2976392) reduces transcriptional activity of an upstream fragment of the gene [OMIM:PROSTATE STEM CELL ANTIGEN; PSCA] [GWAS:Bladder cancer]
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
1.6x higher risk for diffuse gastric cancer
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rs2227692, also known as c.1162+162C>T, is a SNP in the SERPINE1 gene. A study of 612 Korean patients with gastric cancer concluded that the rs2227692 C/T and T/T genotypes had 1.6x greater risk for diffuse gastric cancer than the C/C genotype (p = .00084).
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rs2976392 and diffuse-type gastric cancer (allele-specific odds ratio (OR) = 1.62, 95% CI = 1.38-1.89, P = 1.11 x 10(-9)). Substitution of the C allele with the risk allele T at a SNP in the first exon (rs2294008, which has r(2) = 0.995, D' = 0.999 with rs2976392) reduces transcriptional activity of an upstream fragment of the gene [OMIM:PROSTATE STEM CELL ANTIGEN; PSCA]
Frequency: 45.3%
References:1
References:1
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rs12479919(A;A) genotype had a 41% lower risk of gastric cancer (OR)=0.59, 95% confidence interval (CI): 0.36-0.95; P trend=0.06
1.4x increased gastric cancer risk. Increased risk of Acute Graft-Versus-Host Disease after Unrelated Bone Marrow Transplantation
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rs2275913, also known as G-197A, is a SNP in the IL17A gene. A study of 811 Japanese subjects (524 without gastric cancer and 287 with gastric cancer) reported an odds ratio of 1.42 (CI: 1.09-1.85, p=0.01) for the rs2275913(A) allele, and 3.02 (CI: 1.86-4.91, p<0.0001) for the (A;A) genotype, with gastric cancer. This 'A'-allele of this SNP is also functionally associated with acute Graft-Versus-Host Disease after unrelated bone marrow transplantation
among patients with gastric cancer, risk for more aggressive form?
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rs187116, also known as +4883G>A, is a SNP in the CD44 gene. A presentation at the 2010 American Society of Clinical Oncology meeting based on ~100 patients reported this SNP as being significantly associated with more aggressive gastric cancer. In dbSNP orientation, the risk allele is rs187116(C); patients carrying at least one rs187116(C) had a significantly shorter median time-to-recurrence (TTR) of 2.1 years compared to 7.0 years TTR for rs187116(T;T) patients (p = 0.036, log-rank test).[http://www.asco.org/ASCOv2/Meetings/Abstracts?&vmview=abst_detail_view&confID=72&abstractID=1689]
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source rs1230025 and more than 3 beers per day linked to a 75% increased risk of developing gastric cancer. Wine were liquor not associated.
normal
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rs2274223 is a SNP in the phospholipase C, epsilon 1 PLCE1 gene. In a large study of Han Chinese esophageal cancer patients [specifically esophageal squamous cell carcinoma (ESCC)], the rs2274223(G) allele was associated with greater risk (odds ratio 1.43, p = 7.4 x 10e-56).In this same study [http://www.nature.com/ng/journal/vaop/ncurrent/ris/ng.648.ris, rs2274223(G) was also associated with greater risk for gastric cancer (aka stomach cancer), with an odds ratio of 1.55 (1.74 x 10e-39). [OMIM:?] [GWAS:None]
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
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influences mitosis associated with cancer * breast cancer * colorectal cancer * gastric cancer
normal risk
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rs1799724, a SNP near the tumor necrosis factor TNF gene, was found in a study of ~500 Caucasians to be both an independent risk factor for the development of Alzheimer's disease and also a modifier of the risk for individuals carrying ApoE4 alleles. On its own, the rs1799724(T) allele led to an odds ratio of 1.63 (CI: 1.13-2.34, p=0.009). In carriers of ApoE4 alleles, the odds ratio changed from 2.92 (CI: 2.00-4.27) in the absence of rs1799724(T) to an OR of 6.65 (CI: 3.26-13.55, p=0.03) in its presence. In a Chinese study , post-menopausal women were significantly more likely to have low bone mineral density if they had *CC-AA genotypes in rs1799724-rs1800629 * a haplotype of rs1799724-rs1800629-rs6254-rs6256-IL-1ra-rs2227956-rs1801197 news cigarette smoking and gastric cancer risk [Pha...
12 snps
(hide) Gaucher's disease
common in clinvar
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rs364897, also known as Asn188Ser or N188S, is a variant in the GBA gene. rs354897(A) encodes the more common Asn at this position. rs364897(G;G) has been observed in Korean and Taiwanese subjects with type I Gaucher disease. It may be a relatively mild defect in the gene, since it appears the encoded enzyme appears to retain most of its function. [OMIM:?]
common in clinvar
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rs2230288, also known as E326K or E365K, is a variation in the GBA gene which appears to be well tolerated; in other words, it is not associated with Gaucher disease. However, there is some evidence suggesting it is not a neutral polymorphism; instead, it appears to be a 'modifier' variant. [OMIM:?]
normal
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i4000386, also known as R496H (risk genotype AA) Possibly associated with Gaucher's disease. Gaucher Disease rs80356773
normal
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i400415, also known as N370S (risk genotype CC) Possibly associated with Gaucher's disease. * Type I (N370S homozygote), the most common, also called the 'non-neuropathic' type occurs mainly in Ashkenazi Jews, at 100 times the occurrence in the general populace. The median age at diagnosis is 28 years of age, and life expectancy is mildly decreased. There are no neurological symptoms. rs76763715 Parkinson's disease Gaucher Disease
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i4000417, also known as 84GG (risk genotype GG) Associated with Gaucher's disease. Outside of 23andMe, the rest of the world calls this SNP rs387906315. Gaucher Disease rs387906315
normal
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i4000419, also known as V394L (risk genotype AA) Possibly associated with Gaucher's disease. Gaucher Disease rs80356769
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common/normal
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rs1064651, also known as Asp448His or D448H, is a SNP in exon 9 of the GBA gene on chromosome 1. As the protein was originally numbered, though, this variation occurred at amino acid 409 (rather than 448), so the scientific literature still often refers to this mutation as Asp409His or D409H. Mutations in both copies of a person's GBA gene may lead to Gaucher's disease, an autosomal recessive disorder. When one of the mutations is the D409H mutation, the clinical description may be Gaucher disease type 3C, involving valvular heart disease. However, the clinical presentation appears to be highly variable as well as dependent on which two mutations are present. For more information, see OMIM 606463.0006. Be aware that since this mutation is due to a G>C (tranversion) when oriented in the ...
9 snps
(hide) GERD
some risk linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil).
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
normal Eosinophilic esophagitis (EE) is an emerging worldwide disease, as documented by recent case series from Switzerland, Australia, Canada, Japan, England, and the US (1–4). Of concern, EE appears to be a growing health problem with an annual incidence of at least 1 in 10,000 children (5). The primary symptoms of EE (chest and abdominal pain, dysphagia, heartburn, vomiting, and food impaction) are also observed in patients with chronic esophagitis (CE) including gastroesophageal reflux disease (GERD) (6–8). However, in contrast to GERD, EE occurs more frequently in males (80%), appears to have a common familial form, has a high rate of associated atopic disease (70%), and is typically associated with a normal pH probe recording of the esophagus (5, 9, 10) In the 3? untrans...
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rs2302009 is a SNP located in the 3' untranslated region of the CCL26 gene. This gene (and this SNP) were discovered to be strongly associated with 117 patients with eosinophilic esophagitis, a form of esophagitis (or inflammation of the esophagus) that shares many symptoms with gastroesophageal reflux disease (GERD). rs2302009(G) is the risk allele. The rs2302009(G;G) homozygous genotype is the most predisposed to developing eosinophilic esophagitis (odds ratio 4.55, CI 1.71–12.39). The heterozgyote (rs2302009(G;T)) genotype's risk was indistinguishable statistically from the normal rs23020099(T;T) genotype. [OMIM:ESOPHAGITIS, EOSINOPHILIC]
2 snps
(hide) Gestational diabetes
Magnitude: 2.5
Frequency: 38.9%
Repute:Bad
References:118
Frequency: 38.9%
Repute:Bad
References:118
increased risk for type-2 diabetes
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rs13266634 is a SNP in the zinc transporter protein member 8 SLC30A8 gene that has primarily been associated with type-2 diabetes in several studies. This SNP is also known as the Arg325Trp or R325W variant; the (C) allele encodes the arginine (R), and the (T) allele encodes the tryptophan (W). significantly associated p = 0.0073; in 1,630 Japanese subjects with type-2 diabetes and in 1,064 controls The major alleles of the SLC30A8 SNP rs13266634 and the HHEX SNP rs7923837 associate with reduced insulin secretion, but not with insulin resistance. 46% of European non-diabetic offspring of type-2 diabetes patients are rs13266634(C;C) homozygotes; they are diabetes-prone and characterised by a 19% decrease in first-phase insulin release following an intravenous glucose load. * Note: this SNP,...
1.2x increased risk for type-2 diabetes
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rs4402960 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.23 (CI: 1.11-1.36, p = 8.1 x 10e-5) associated with type-2 diabetes significantly associated with type-2 diabetes p = 0.00009; in 1,630 Japanese subjects and in 1,064 controls 1,638 type-2 diabetes patients and 1,858 controls *rs4402960 borderline (OR 1.10, 95% CI: 0.99-1.22). Neither rs4402960 or rs1470579 were found to be associated with type-2 diabetes in a study of 3,000 French Caucasians. This SNP was confirmed to be associated with type-2 diabetes in a study of 500+ Japanese patients plus pooled meta-analysis with 6 previous association studies (also of Japanese). Note: rs4402960 is fairly tightly linked (r<sup>2</sup>=0.87) with another IGF2BP2 gene SNP also asso...
Magnitude: 2
Frequency: 29.2%
Repute:Bad
References:107
Frequency: 29.2%
Repute:Bad
References:107
1.2x increased risk for type-2 diabetes
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rs10811661 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.27 (CI: 1.15-1.40, p = 1.9 x 10e-6) rs10811661 is mentioned in part 2 of a series significantly associated with type-2 diabetes p = 0.0024; in 1,630 Japanese subjects with type-2 diabetes and in 1,064 controls 1,638 type 2 diabetes patients and 1,858 controls *rs10811661 in the vicinity of CDKN2B (OR 1.20, 95% CI: 1.06-1.37, p = 0.004) T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for *CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) *CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) *IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, in...
3.2x risk for T2D
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rs7923837 is a SNP of the HHEX homeobox gene. In several studies, it has been associated with risk for type-2 diabetes (T2D). In a study of 500 unrelated Caucasian T2D patients, the rs7923837(G) allele was overrepresented; the odds ratio was 1.57 (CI: 1.08-2.27, p=0.017). In this population, the population attributable risk for this allele was estimated to be 33%. In a study of ~400 Japanese T2D patients, rs7923837(G) was also associated with type-2 diabetes (odds ratio 1.66, CI: 1.28-2.15, p=0.00014). Heterozygous and homozygous carriers of the risk allele had odds ratios of 1.57 (95% CI 1.15-2.16, p=0.0050) and 3.16 (95% CI 1.40-7.16, p=0.0038) relative to non-carriers. rs7923837 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.27 (CI: 1...
Normal (lower) risk of Type 2 Diabetes and Gestational Diabetes. Normal insulin secretion in the pancreas. This has been confirmed in most races.
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This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). This SNP is also known as IVS3C>T. rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. Full text of the paper is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse population Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion...
lower risk of obesity and Type-2 diabetes
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rs9939609 is a SNP in the fat mass and obesity associated FTO gene, aka the 'Fat Gene' The original paper describing it is here . [http://www.alzforum.org/new/detail.asp?id=1567 The researchers identified 10 different FTO SNPs in the first intron of the gene that associated with both BMI and type-2 diabetes. Because they all correlated with each other, they chose to examine one of the SNPs (rs9939609) in detail. rs9939609 has also been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.34 (CI 1.17-1.52), and for homozygotes, 1.55 (CI 1.3-1.84). In a different study, this SNP was found in a linkage block in the FTO gene with rs1121980; see rs1121980 for the association of th...
1.2x increased risk for type-2 diabetes
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rs1470579 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.18 (CI: 1.07-1.31, p = 8.3 x 10e-4) T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for *CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) *CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) *IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24) Neither rs4402960 or rs1470579 were found to be associated with type-2 diabetes in a study of 3,000 French Caucasi...
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related to Prostate cancer] and Type-2 diabetes The increased risk associated with rs7501939 and the closely linked rs4430796 is approximately doubled in individuals hereditarily predisposed to develop early-onset prostate cancer, based on a study of ~1,000 men. rs7501939 identified as one of three HNF1B gene SNPs associated with decreased risk for prostate cancer in two large prospective studies cancer-genetics these SNPs influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 [OMIM:PROSTATE CANCER, HEREDITARY, 11; HPC11] [GWAS:Prostate cancer]
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[GWAS:Type 2 diabetes]
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associated with type-2 diabetes, but then called into question by along with rs9300039 rs4402960 rs7754840 rs17044137 rs11037909 rs1081161 rs1111875 rs7923837 rs12885713 rs1219648 rs2981582 [PharmGKB:Non-Curated GWAS Results: Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes (Initial Sample Size: 1,924 cases, 2,938 controls; Replication Sample Size: 3,757 cases, 5,346 controls; Risk Allele: rs5015480-C).] [GWAS:Type 2 diabetes] [GWAS:Type 2 diabetes]
2.4x risk of [[type-2 diabetes]]
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rs1111875 is a SNP of the HHEX homeobox gene. In several studies, it has been associated with risk for type-2 diabetes (T2D). In a study of 500 unrelated Caucasian T2D patients, the rs1111875(G) allele was overrepresented; the odds ratio was 1.68 (CI: 1.19-2.35, p=0.003). In this population, the population attributable risk for this allele was estimated to be 36%. In a study of ~400 Japanese, rs1111875(G) was also associated with type-2 diabetes (odds ratio 1.42, CI: 1.13-1.78, p=0.0024). Heterozygous and homozygous carriers of the risk allele had odds ratios of 1.31 (CI: 0.97-1.77, p=0.0810) and 2.40 (CI: 1.34-4.32, p=0.0028) relative to non-carriers. And in a third study, 1,630 Japanese patients were also found to have this SNP significantly overrepresented (p=0.0064). rs1111875 replicat...
1.3x increased risk for type-2 diabetes
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Polycystic Kidney disease rs7756992 significantly p = 0.0363 associated with type-2 diabetes in 1,630 Japanese subjects and in 1,064 controls rs7756992 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.27 (CI: 1.15-1.40, p = 9.8 x 10e-7) 1,638 type 2 diabetes patients and 1,858 controls *rs7756992 non-significant T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for *CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) *CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) *IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined...
1.16x increased risk for type-2 diabetes
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rs3802177 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.16 (CI: 1.05-1.27, p = 4.5 x 10e-3) Note: this SNP is fairly tightly linked (r<sup>2</sup> = 0.83) to another SNP in the SLC30A8 gene also linked to type-2 diabetes, rs13266634 [GWAS:Type 2 diabetes]
Frequency: 42.5%
References:12
References:12
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Replication of the association between variants in WFS1 and risk of type 2 diabetes in European populations. Testing of diabetes-associated WFS1 polymorphisms in the Diabetes Prevention Program. Association analysis of type 2 diabetes Loci in type 1 diabetes. Assessing the combined impact of 18 common genetic variants of modest effect sizes on type 2 diabetes risk. Predicting type 2 diabetes based on polymorphisms from genome-wide association studies: a population-based study. Clinical review: the genetics of type 2 diabetes: a realistic appraisal in 2008. Common type 2 diabetes risk gene variants associate with gestational diabetes. Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data. Novel association of HK1 with glycated...
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[PharmGKB:Non-Curated GWAS results: A variant near MTNR1B is associated with increased fasting plasma glucose levels and type 2 diabetes risk. (Initial Sample Size: 2,151 individuals; Replication Sample Size: 6,332 cases, 9,132 controls); (Region: 11q21; Reported Gene(s): MTNR1B; Risk Allele: rs1387153-T); (p-value= 2E-36).This variant is associated with Fasting plasma glucose.] [OMIM:?] [GWAS:Fasting plasma glucose]
Frequency: 50.8%
Repute:Bad
References:60
Repute:Bad
References:60
increased type-2 diabetes risk; higher gestational diabetes risk
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rs10830963 was associated with an increased risk of type-2 diabetes in our Han Chinese cohort (OR 1.16, 95% CI 1.03-1.31, p = 0.015). As previously described, the risk variant was also associated with increased fasting plasma glucose, showing an increase of 0.068 mmol/l (95% CI 0.036-0.100, p = 4 x 10(-5)) per risk allele rs10830962, rs4753426, and rs10830963 were significantly associated with higher fasting plasma glucose concentrations and reduced OGTT- and IVGTT-induced insulin release. rs3781638 displayed significant association with lower fasting plasma glucose levels and increased OGTT-induced insulin release A study totaling 19,000+ Europeans concluded that rs10830963 had the most influence of any MTNR1B gene SNP on the risk for type-2 diabetes. Specifically, the (G) allele increase...
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summary, indicating a small effect of this SNP, seen only in meta-analyses rs3792267 associated with noninsulin-dependent diabetes mellitus, polycystic ovary syndrome, type 2 diabetes, gestational diabetes and obesity [OMIM:CALPAIN 10; CAPN10]
normal fat metabolism; common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
normal
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rs5219, also known as E23K, is a SNP in the KCNJ11 gene. The association between type-1 diabetes and rs5219 is mentioned as being replicated in ; there is also a 90% correlation between rs5219 and rs5215. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under an additive model, the odds ratio for the minor (risk) allele (T) is 1.15 (CI: 0.95-1.4, p=0.2, ie not significant). But for the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). Genotyping of ~4000 Chinese as well a meta-analysis concluded that rs5219 was associated with type-2 diabet...
normal
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The accuracy of claims about this snp are called into question by table 1 of discusses the process of including this snp into Coriell and raises some doubt about the value of its inclusion. rs7754840 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.28 (CI: 1.17-1.41, p = 4.5 x 10e-7) type-2 diabetes Carriers of the (C;G) and (C;C) genotypes of rs7754840 had 11% and 24% lower first-phase insulin release in an IVGTT compared to that in carriers of the (G;G) genotype (P=0.002). The C allele was also associated with higher glucose area under the curve in an OGTT (P=0.016). rs7754840 type-2 diabetes Ashkenazi Jewish population shows an even stronger effect for rs7754840 than the general Caucasian population, based on 1,131 cases versus 1,147 co...
20 snps
(hide) Gilbert syndrome
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Xenobiotic metabolizing gene variants, dietary heterocyclic amine intake, and risk of prostate cancer. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. [OMIM:UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEPTIDE A1; UGT1A1] [GWAS:Serum bilirubin levels]
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The (C;C) genotype is linked to reduced UGT1A1 activity, and increased Bilirubin, except in people of African origin for whom the T allele is a risk factor for breast cancer. [Genetic polymorphisms of MPO, NQO1, GSTP1, UGT1A6 associated with susceptibility of chronic benzene poisoning]. The influence of metabolic gene polymorphisms on urinary 1-hydroxypyrene concentrations in Chinese coke oven workers. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [Relationship between genetic polymorphisms of phase I and phase II metabolizing enzymes and DNA damage of workers exposed to vinyl chloride monomer]. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. Pazopanib-induced hyp...
normal
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Something seems wrong between dbSNP and the results from 23andMe and FTDNA. See Talk:Rs4148323 for more information. rs4148323, a SNP also known as 211G>A or G71R, occurs in the UGT1A1 gene, and defines the UGT1A1*6 allele. This allele is associated with Gilbert's syndrome among Asians, Crigler-Najjar syndrome type II (CN-II), and transient familial neonatal hyperbilirubinemia. rs4148323(A) in exon 1 of the UGT1A1 gene is associated with hyperbilirubinemia. rs4148323 and several other nearby SNPs help predict serum total bilirubin levels, based on a study of 750 Japanese. [PharmGKB:Curated *6 is the most common UGT1A1 coding variant found in Asians. It may result in reduced capacity to metabolize irinotecan and hence irinotecan toxicity.] [OMIM:UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEP...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
4 snps
(hide) Glaucoma
common but 10x higher glaucoma risk in most (but not all) populations This genotype is found in 2 out of 3 people, but has been repeatedly linked to a much higher risk of glaucoma. However a 2010 paper in a south african population reports reduced risk, casting some doubts.
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rs3825942, also known as G153D, a SNP causing an amino acid change in the lysyl oxidase 1 LOXL1 gene, has been linked to exfoliation glaucoma (also known as exfoliation syndrome). This form of glaucoma causes up to 10% of the cases of blindness in many countries, including the US. From the abstract of this study: 'Approximately 25% of the general population is homozygous for the highest risk haplotype [C;C here combined with other risk SNPs] and their risk of suffering XFG (exfoliation glaucoma) is over 100 times that of those only carrying low-risk haplotypes.' The risk allele for this SNP is rs3825942(C), as oriented with respect to the dbSNP entry, and it confers a estimated relative risk (by itself) of 27 compared to the (T) allele. The odds ratio is 20.10 (CI 10.80-37.41). [Note that ...
4.4x increased risk of exfoliation glaucoma glaucoma risk likely to actually be based on nearby rs3825942
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This SNP, located in an intron of the LOXL1 gene, was initially reported to be associated with exfoliation glaucoma. However, it was shown in the same study to no longer be significant once two other SNPs, which cause actual changes in the LOXL1 protein, were identified. More specifically, the risk allele rs2165241(T) was found to be associated with glaucoma only because it effectively predicted (with 90% probability) the actual high-risk haplotype consisting of rs1048661(G) and rs3825942(C), as oriented with respect to their entries in dbSNP. However, a meta-analysis published in 2010 concluded that it's likely that SNPs rs1048661 and rs2165241 are not directly implicated in the pathogenesis of glaucoma; only the nearby rs3825942 seemed to be the disease-associated SNP. rs2165241 was sign...
Frequency: 28.3%
References:5
References:5
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23andMe blog citing in an Afro-Caribbean population rs12994401(T;T) had almost 35 times higher odds of primary open-angle glaucoma. This correlation was not found in Japanese , Korean , Chinese , African or Central European populations. In African-American population correlation was for the reverse allele C. This suggest as yet unidentified causal variant with population dependent linkage to rs12994401 is responsible . South-Indian cohort evaluation suggests rs10202118 as one contributor, while Chinese study suggests rs1533428 contribution. However, an analysis of extended chromosome locus 2p14-21 did not find such association, and meta-analysis by the Chinese study showed insignificant association to rs12994401 overall.
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rs4977756 is a SNP near the CDKN2BAS gene. A (GWA) study for open-angle glaucoma (OAG) blindness ultimately based on ~1500 cases concluded that the rather common rs4977756(A) allele was statistically associated with the condition, with a per allele odds ratio of 1.39 (CI: 1.28–1.51, p = 1.35 × 10e?14). [OMIM:?] [GWAS:Glioma]
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23andMe blog rs1533428(T;T) had 7x odds of glaucoma
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Glaucoma
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association with exfoliation glaucoma; possible genoset partner with rs2165241
possibly higher glaucoma risk? glaucoma risk likely to actually be based on nearby rs3825942
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rs1048661, also known as R141L, a SNP causing an amino acid change in the lysyl oxidase 1 LOXL1 gene, has been linked to exfoliation glaucoma. This form of glaucoma causes up to 10% of the cases of blindness in many countries, including the US. [Science DOI: 10.1126/science.1146554] From the abstract of this study: 'Approximately 25% of the general population is homozygous for the highest risk haplotype and their risk of suffering XFG (exfoliation glaucoma) is over 100 times that of those only carrying low-risk haplotypes.' The risk allele for this SNP is rs1048661(G), and it confers a estimated relative risk (by itself) of 3.04. The odds ratio is 2.46 (CI 1.91-3.16). [Note that the (G) allele is actually quite common in most European populations.] However, a meta-analysis published in 201...
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
normal
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rs4656461 is a SNP near the TMCO1 gene. A (GWA) study for open-angle glaucoma (OAG) blindness ultimately based on ~1500 cases concluded that the rather rare rs4656461(G) allele was statistically associated with the condition, with a per allele odds ratio of 1.5 (CI: 1.35–1.68, p = 6 × 10e?14).
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
14 snps
(hide) Glioma
higher risk of Interstitial lung disease, and testicular cancer
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23andMe blog rs2736100 C 1.27 Glioma Lung cancer susceptibility locus at 5p15.33. Common genetic variants on 5p15.33 contribute to risk of lung adenocarcinoma in a Chinese population. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study. Role of 5p15.33 (TERT-CLPTM1L), 6p21.33 and 15q25.1 (CHRNA5-CHRNA3) variation and lung cancer risk in never-smokers. Individuals susceptible to lung adenocarcinoma defined by combined HLA-DQA1 and TERT genotypes. New insights into susceptibility to glioma. Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium. Evaluatio...
1.4x higher risk for glioma development; but this is the common allele
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'''rs6010620''' is a SNP associated with atopic dermatitis (AD). Also known as eczema, AD is one of the most common chronic inflammatory skin disorders with a prevalence estimated up to 20% in children and 3% in adults . It is a complex and highly heterogeneous disease that likely involves various genetic factors. The SNP rs6010620 locates on chromosome 20q13.33, at which there are eight genes — ''PRIC285'', ''STMN3'', ''RTEL1'', ''TNFRSF6B'', ''ARFRP1'', ''ZGPAT'', and ''LIME1'' —, within a single 200-kb LD block around rs6010620. Among them, ''TNFRSF6B'' and ''ZGPAT'' might be the susceptibility candidates whose expressions correlate with the SNP as suggested by expression quantitative trait loci (eQTL) analysis . rs6010620’s association with AD was first identified in ...
1.2x higher risk for glioma development
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23andMe blog rs498872 A 1.18 Glioma [GWAS:Glioma]
1.2x higher risk for glioma development
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Associated with glioma risk. Genetic causes of glioma: new leads in the labyrinth. [GWAS:None]
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23andMe blog rs1412829 G 1.22 Glioma [OMIM:?] [GWAS:Glioma (high-grade)]
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rs4977756 is a SNP near the CDKN2BAS gene. A (GWA) study for open-angle glaucoma (OAG) blindness ultimately based on ~1500 cases concluded that the rather common rs4977756(A) allele was statistically associated with the condition, with a per allele odds ratio of 1.39 (CI: 1.28–1.51, p = 1.35 × 10e?14). [OMIM:?] [GWAS:Glioma]
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[GWAS:Glioma]
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[GWAS:Glioma]
Magnitude: 0
Frequency: 67.3%
Repute:Good
References:4
Frequency: 67.3%
Repute:Good
References:4
common in complete genomics
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Associated with glioma risk. Genetic causes of glioma: new leads in the labyrinth. [GWAS:None]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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rs78378222[C] (odds ratio (OR) = 2.36, P = 5.2 × 10?17). rs78378222 is in the 3? untranslated region of TP53 and changes the AATAAA polyadenylation signal to AATACA, resulting in impaired 3?-end processing of TP53 mRNA. Investigation of other tumor types identified associations of this SNP with prostate cancer (OR = 1.44, P = 2.4 × 10?6), glioma (OR = 2.35, P = 1.0 × 10?5) and colorectal adenoma (OR = 1.39, P = 1.6 × 10?4). However, we observed no effect for breast cancer, a common Li-Fraumeni syndrome tumor (OR = 1.06, P = 0.57, 95% confidence interval 0.88–1.27). [GWAS:Basal cell carcinoma]
10 snps
(hide) Glycogen storage disease type 1A
common in clinvar
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rs1801175, also known as R83C or Arg83Cys, is a SNP in the glucose-6-phosphatase G6PC gene. The common allele is rs1801175(C). Observed to date primarily in Ashkenazi Jews, at a frequency of about 1 in 100, the rs1801175(T) allele is associated with Glycogen storage disease type 1A; heterozgyotes are unaffected carriers, homozygote rs1801175(T;T) will have the disease. However, the mutation alone does not predict the severity of the disease. Note that 23andMe tests for this SNP using their own terminology (i3002486). See also: OMIM 232200.0002 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
3 snps
1 snp
(hide) Gout
normal, but increased risk of gout
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risk for cardiovascular morbidity and mortality rs6855911 (p = 1.84E-16) although no risk for coronary artery disease or myocardial infarction was observed, rs6855911 was associated with gout. The minor allele had a protective effect, with an allelic odds ratio of 0.62 (CI: 0.52-0.75, p = 3.2x10(-7)). [PharmGKB:Non-Curated GWAS Results: The GLUT9 Gene Is Associated with Serum Uric Acid Levels in Sardinia and Chianti Cohorts (Initial Sample Size: 4,305 Sardinian individuals; Replication Sample Size: 1,301 Tuscan individuals; Risk Allele: rs6855911-A). This variant is associated with serum urate levels.] [GWAS:Serum urate]
Magnitude: 1.5
Frequency: 57.5%
Repute:Bad
References:2
Frequency: 57.5%
Repute:Bad
References:2
1.25 increased risk for gout
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Each copy of the minor (G) allele appears to confer reduced risk for gout based on combined data from over 140,000 individuals of European ancestry within the Global Urate Genetics Consortium (GUGC), replicating an association reported earlier for a linked SNP in this gene. [GWAS:Urate levels]
0.85x decreased gout risk
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rs1165205 is a SNP in the SLC17A3 gene on ch 6. A large study totaling 7,699 participants in the Framingham cohort and 4,148 participants in the Rotterdam cohort was conducted, with genome-wide significant SNPs then replicated in 11,000+ Caucasian and ~4,000 African-American individuals who took part in the study of Atherosclerosis Risk in Communities (ARIC). This study calculated an odds ratio of 0.85 for rs1165205, (CI: 0.77-0.94, p = 0.002). A genetic score comprised of this SNP plus 2 others may stratify risk for gout. See also: 23andMe blog gout *rs2231142(T) 1.7x *rs16890979(C) 1.7x *rs1165205(A) 1.2x [PharmGKB:Non-Curated Association of three genetic loci with uric acid concentration and risk of gout: a genome-wide association study. (Initial Sample Size: 11,847 individuals; Replic...
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DeCode reports that the rs737267(G;T) genotype is associated with 0.77 times the normal risk of gout, and the rs737267(G;G) genotype is associated with 1.25 times higher risk of gout. [PharmGKB:Non-Curated GWAS Results: SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout (Initial Sample Size: 794 individuals; Replication Sample Size: 706 individuals; Risk Allele: rs737267-C).] [OMIM:SOLUTE CARRIER FAMILY 2 (FACILITATED GLUCOSE TRANSPORTER), MEMBER] [GWAS:Serum urate]
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[GWAS:Gout]
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Gout (A) increased risk.
Frequency: 59.1%
References:10
References:10
3.4x risk of gout
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rs16890979 has been found to be associated with gout in several independent studies. It may be a variation in the SLC2A9 gene, which is more commonly known as GLUT9. In a study of Old Order Amish, rs16890979 - which is also known as the missense mutation Val253Ile - was found as the most significantly associated SNP during a follow-up study based on a genome wide association study. Each copy of the minor allele, rs16890979(T), was associated with a decrease of 0.47 mg/dl in the uric acid level (CI: 0.31-0.63, p = 1.43 x 10e-11). See also: 23andMe blog gout Independently, a large study totaling 7,699 participants in the Framingham cohort and 4,148 participants in the Rotterdam cohort was conducted, with genome-wide significant SNPs then replicated in 11,000+ Caucasian and ~4,000 African-Ame...
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gout association only due to linkage to rs2231142, according to
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The T allele of rs1260326 has been associated with type 2 diabetes and hypertriglyceridemia. A fine mapping approach indicates that this SNP, rs1260326, shows the strongest association signal with metabolic phenotypes in the region that also harbors the tightly linked (r(2)=0.93) SNP rs780094, which has been previously associated with triglyceride and glucose concentrations. This SNP, rs1260326, encodes a common missense glucokinase regulatory protein gene GCKR variant. gout association, based on Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. The common P446L polymorphi...
normal
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This is basically a surrogate for rs7442295, and thus associated with higher serum urate levels. [OMIM:SOLUTE CARRIER FAMILY 2 (FACILITATED GLUCOSE TRANSPORTER), MEMBER] [GWAS:Uric acid levels]
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23andMe blog each G at rs4293393 decreased the odds of chronic kidney disease by 24%. Approximately 18% of people with European ancestry have at least one G at this SNP. DeCode reports that the T allele of rs4293393 is associated with kidney stones and chronic kidney disease. This SNP may also be associated with susceptibility to gout], hypertension, and diabetes.
normal
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rs2231142, also known as Q141K and C421A, is a SNP in the ABCG2 gene, indicating a missense variant. 'Our data indicate that at least 10% of all gout cases in whites are attributable to this causal variant.' A is the risk allele. A large study totaling 7,699 participants in the Framingham cohort and 4,148 participants in the Rotterdam cohort was conducted, with genome-wide significant SNPs then replicated in 11,000+ Caucasian and ~4,000 African-American individuals who took part in the study of Atherosclerosis Risk in Communities (ARIC). This study calculated an odds ratio of 1.74 for rs2231142 (CI: 1.51-1.99, p = 3.3x10e-15). A genetic score comprised of this SNP plus 2 others may stratify risk for gout. Among non-small cell lung cancer patients treated with gefitinib, there's a 4-5x high...
common in complete genomics
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A gene-wide investigation on polymorphisms in the ABCG2/BRCP transporter and susceptibility to colorectal cancer. [GWAS:None]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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rs72552713, also known as Gln126Ter, is a SNP in the ABCG2 gene. gout association, based on ; note that this publication refers to risk allele (T) based on the minus strand, whereas for dbSNP and SNPedia, rs72552713 is defined as on the plus strand, so therefore the risk allele is (A). The case-control analysis of 1993 patients with gout and 1334 controls concluded that rs72552713(A) was significantly associated with gout (odds ratio 2.86, CI:2.1-3.8,p=4.4x10e-12). The risk is independent of the risk posed by another ABCG2 gene SNP, rs2231142, since these two SNPs are on different haplotypes. Both ABCG2 SNPs are, however, associated with the ROL gout subtype, defined as when urinary urate excretion (UUE) is over 25.0 mg/h/1.73 m2 (600 mg/day/1.73 m2) and urate clearance (urate clearance/cr...
14 snps
(hide) Graves' disease
1.5x increased risk for Crohn's disease; 2x increased risk for Graves' disease
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SNP rs2201841, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. Another study found that the 'A allele' and 'AA genotype' were significantly overrepresented in Graves' disease patients with Graves ophthalmopathy, based on 216 North American patients. The odds ratios reported were 2.04 for the allele (p=1x10<sup>-4</sup>), and for the so-called 'AA' genotype (presumably rs2201841(T;T) when correctly oriented to the dbSNP orientation), 2.4 (p=1x10<sup>-4</sup>). 23andMe blog psoriasis Europeans *rs2201841(G) 1.13x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication S...
Magnitude: 2
Frequency: 38.9%
Repute:Bad
References:40
Frequency: 38.9%
Repute:Bad
References:40
1.5x increased risk for certain autoimmune diseases; 2x increased risk for Graves disease
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SNP rs10889677, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele for this SNP has been associated with increased risk for ankylosing spondylitis in a large study of over 1,000 Caucasian patients. The odds ratio is 1.3 (p=1.3x10e-6). In a study of 216 North American patients with Graves' disease, the C allele of rs10889677 was 2.03x overrepresented (p=1.3x10<sup>–4</sup>), and the homozygous rs10889677(C;C) genotype was also overrepresented (2.36x; p=1.4x10<sup>-4</sup>) in Graves ophthalmopathy patients. A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ance...
blood type O
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=Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women. |OA=23andMe blog each copy rs505922(C) is associated with 1.2x risk of pancreatic cancer influences ABO blood group [PharmGKB:Non-Curated GWAS results: Common susceptibility allele are unlikely to contribute as strongly as the FV and ABO loci to VTE risk: results from a GWAS approach. (Initial Sample Size: 419 cases, 1,228 controls; Replication Sample Size: 1,757 cases, 1,480 controls); (Region: 9q34.2; Reported Gene(s): ABO; Risk Allele: rs505922-C); (p-value= 0.000000000000004).This variant is associated with Venous thromboembolism.] [OMIM:?] [GWAS:Venous thromboembolism]
2.1x risk for Aspirin Induced Asthma. But possibly lower risk of intractible Grave's disease. Only tested in Japanese people. Might not be true for other races. May also be slightly protective against lupus (in Chinese people).
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rs4794067(C;C) and rs4794067(C;T) genotypes for the TBX21 gene are calculated to be at 2.15 fold higher risk (CI: 1.26-3.64) for aspirin-induced asthma (AIA) compared to rs4794067(T;T) homozygotes, based on a study of 72 patients vs 640 controls in a study of a Japanese population. Note that in this population, but perhaps not others, linkage disequilibrium exists between this SNP located upstream of the gene, rs4794067, and a common synonymous SNP located in the first exon, rs2074190, with a predictive accuracy of 92%. On the other hand, rs4794067(C;C) may greatly decrease the risk of lupus if rs17250932(C;C) is also present (at least in Chinese people). And those 2 SNPs also reduce the risk of intractable Graves' disease (at least in Japanese people).
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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. [GWAS:Vitiligo]
1.8x increased lupus risk
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rs1800630 is a SNP upstream of the tumor necrosis alpha (TNF) gene; this SNP is also typically called the -863 variant. In a study of 154 Thai patients with systemic lupus erythematosus (SLE), rs1800630(A) allele frequency was significantly increased, with an odds ratio of 1.85 (CI: 1.21-2.83, p(corr) = 0.009). This allele was also found to be significantly increased in the SLE group with Raynaud's phenomenon compared to SLE without Raynaud's phenomenon ( odds ratio of 2.23, CI: 1.21-4.10, p(corr) = 0.048). Separately, a meta-analysis of 10 case-control studies, including over 2,200 Graves' disease cases, concluded that rs1800630(A) carriers were associated with the disease.
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Associated with at least one 'mortality outcome' in a study of ~10,000 individuals. Separately, a meta-analysis of 10 case-control studies, including over 2,200 Graves' disease cases, concluded that rs1799964(C) carriers were associated with the disease. [PharmGKB:Curated Haplotype tagging SNP.] [GWAS:Crohn's disease]
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[GWAS:Graves' disease]
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rs231775, also known as +49A/G, is a SNP in the CTLA4 gene. which is linked to Hashimoto thyroiditis In a meta-analysis of CTLA4 gene SNPs, rs231775 was most associated with vitiligo; however, the association seems to hold only in the subgroup of patients with other autoimmune diseases. rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease associated with the development of placental abruption and preeclampsia, with women having the G allele being at risk rs231775 was not associated with type-1 diabetes in a study of 207 Portuguese patients. [PharmGKB:Curated This SNP affects risk for Autoimmune Thyroid Disorder (AITD). The G allele is generally thought to be the risk-conferring allele, but this study found that which allele confers ri...
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This SNP is unclear. According to GWAS one study says risk allele is A, another study says risk allele is C. Ambiguous flip ? Abstract associated with type-1 diabetes, organ-specific autoimmune diseases, including Graves' disease. (odds ratio 1.47 (CI: 1.23–1.76, p = 1.9 x 10<sup>–5</sup>) This polymorphism may also contribute to several other autoimmune disorders. A study of 261 Chinese patients with Graves' disease failed to find any association with rs1990760. A study of 591 French Caucasian multiple sclerosis trio families found no association between rs1990760 or rs2068330 and the disease, which did not confirm one previously reported study. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the...
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[GWAS:Graves' disease]
1.9x increased risk for SLE (lupus)
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rs3748079 is a SNP in the promoter region of the ITPR3 gene; it is also known as -1990C>T. rs3748079 has been linked to increased risk for systemic lupus erythematosus (SLE) in two independent Japanese case-control samples (p=0.0000000178 with odds ratio of 1.88, CI:1.51-2.35). Individuals with risk genotypes of both rs3748079 and rs3095870, in the ITPR3 and NKX2.5 genes, respectively, have even high risk for SLE (odds ratio 5.77). This particular SNP also revealed associations with rheumatoid arthritis (RA) (p=0.0084 with odds ratio of 1.23, CI:1.05-1.43) and with Graves' disease (GD) (p=0.00036 with odds ratio of 1.57, CI:1.22-2.02). Note that the orientation of this SNP as published is reversed compared to the dbSNP entry. [OMIM:SYSTEMIC LUPUS ERYTHEMATOSUS; SLE]
normal for RA; 1.4x increased GD risk
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rs3789604 is associated with increased susceptibility to rheumatoid arthritis, based on a study of ~1,000 Caucasian individuals. The odds ratio is 1.55x for (G;T) heterozygotes and 1.73x for (G;G) homozygotes. However, in a Japanese population, the other allele, rs3789604(T), is associated with increased risk (odds ratio 1.45, p=0.0085) for Graves' disease (GD). [OMIM:?]
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
normal
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rs7528684 has been reported to be associated with rheumatoid arthritis in a Caucasian population, following reports of a similar association in a Japanese population. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 0.95 (CI 0.83-1.08), and for homozygotes, 2.30 (CI 1.64-3.23). In a study of 645 Caucasians from Southern Spain with multiple sclerosis, the rs7528684(G) allele (in dbSNP orientation) was found to be somewhat protective (per allele odds ratio 0.81, CI: 0.70-0.94, p=0.007). In another report , a summary indicates the following regarding disease and odds ratio (OR)for rs7528684: * for rheumatoid arthritis: OR = 2.15 (CI = 1.58–2.93), from 830 cases and 658 controls; * for SLE: OR = 1.49 (CI = 1.16â€...
normal
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IL23R gene SNP, part of a haplotype with rs11209026 associated with psoriasis. In a study of 216 North American patients with Graves' disease, the homozygous rs10889677(T;T) genotype was significantly associated with Graves' disease but not specifically with Graves ophthalmopathy; the odds ratio was 9.4 (p=0.02).
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[GWAS:Graves' disease]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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rs62205366 ( 393T>C ) is a SNP within GNAS (GNAS complex locus - encoding the Gs alpha subunit). differential response to dobutamine (beta-1 / [mild] beta-2 receptor agonist) noted in a Chinese sample of unknown size, individuals homozygous for C displayed greater response as compared to those homozygous for T homozygous TT individuals associated with greater incidence of hyperthyroidism (as well as higher TRAb levels) relapse in a sample of 359 Graves' disease patients
18 snps
(hide) Hashimoto thyroiditis
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rs231775, also known as +49A/G, is a SNP in the CTLA4 gene. which is linked to Hashimoto thyroiditis In a meta-analysis of CTLA4 gene SNPs, rs231775 was most associated with vitiligo; however, the association seems to hold only in the subgroup of patients with other autoimmune diseases. rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease associated with the development of placental abruption and preeclampsia, with women having the G allele being at risk rs231775 was not associated with type-1 diabetes in a study of 207 Portuguese patients. [PharmGKB:Curated This SNP affects risk for Autoimmune Thyroid Disorder (AITD). The G allele is generally thought to be the risk-conferring allele, but this study found that which allele confers ri...
normal
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rs7528684 has been reported to be associated with rheumatoid arthritis in a Caucasian population, following reports of a similar association in a Japanese population. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 0.95 (CI 0.83-1.08), and for homozygotes, 2.30 (CI 1.64-3.23). In a study of 645 Caucasians from Southern Spain with multiple sclerosis, the rs7528684(G) allele (in dbSNP orientation) was found to be somewhat protective (per allele odds ratio 0.81, CI: 0.70-0.94, p=0.007). In another report , a summary indicates the following regarding disease and odds ratio (OR)for rs7528684: * for rheumatoid arthritis: OR = 2.15 (CI = 1.58–2.93), from 830 cases and 658 controls; * for SLE: OR = 1.49 (CI = 1.16â€...
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
3 snps
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associated with higher HDL cholesterol
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C allele is associated with 1.87mg/dl increase in HDL cholesterol (good cholesterol). [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 18q21.1; Reported Gene(s): LIPG; Risk Allele: rs4939883-T); (p-value= 0.000000000000007).This variant is associated with HDL cholesterol.] [GWAS:Cholesterol, total]
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C allele is associated with 1.51mg/dl increase in HDL cholesterol (good cholesterol).
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Apolipoprotein E levels in cerebrospinal fluid and the effects of ABCA1 polymorphisms. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Investigation of variants identified in caucasian genome-wide association studies for plasma high-density lipoprotein cholesterol and triglycerides levels in Mexican dyslipidemic study samples. Genome-wide association of lipid-lowering response to statins in combined study populations. Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration. Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC). [PharmGKB:Non-Curated GWAS results: Comm...
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G allele is associated with 0.82mg/dl increase in HDL cholesterol (good cholesterol). [GWAS:HDL cholesterol]
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[GWAS:HDL cholesterol]
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased LDL cholesterol, increased HDL cholesterol and increased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [Pharm...
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[PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 21,412 individuals; Replication Sample Size: NR); (Region: 9q31.1; Reported Gene(s): ABCA1; Risk Allele: rs3905000-G); (p-value= 0.0000000000009).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
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[GWAS:None]
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[GWAS:None]
Frequency: 17.6%
References:10
References:10
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[GWAS:None]
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rs1799864(G), rs3025058(A) and rs662 were associated with increased risk, and rs1800775(A) with reduced risk of recurrent venous thromboembolism [PharmGKB:Curated Meta-analysis showed weak inverse association with coronary risk for the CETP:-629C>A, A allele.] [OMIM:HIGH DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS] [GWAS:HDL cholesterol]
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http://www.medhours.com/master-gene-controls-fat-metabolism/ The enrichment of rs4731702 trans associations for low P values suggests that KLF14 is a master regulator of gene expression in adipose tissue Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis. [GWAS:None]
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[GWAS:None]
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per the 23andMe blog, the minor allele of this SNP (C) was associated with decreased HDL cholesterol and increased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS result...
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Physiogenomic analysis of weight loss induced by dietary carbohydrate restriction. Physiogenomic comparison of human fat loss in response to diets restrictive of carbohydrate or fat. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Polymorphism in the CETP gene region, HDL cholesterol, and risk of future myocardial infarction: Genomewide analysis among 18 245 initially healthy women from the Women's Genome Health Study. Genetics and beyond--the transcriptome of human monocytes and disease susceptibility. ...
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[PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of HDL-C and apolipoprotein A1. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): HDL-C: p = 1.3 x 10 (-10);ApoA1: p = 9.0 x 10(-14). Type of association: CO; GN] [OMIM:?] [GWAS:Cholesterol, total]
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news three SNPs that appear to have different effects in men and women rs3846662 rs2304130 rs2083637 [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 21,412 individuals; Replication Sample Size: NR); (Region: 8p21.3; Reported Gene(s): LPL; Risk Allele: rs2083637-G); (p-value= 0.000000000000000006).This variant is associated with HDL cholesterol.] [OMIM:LIPOPROTEIN LIPASE; LPL] [GWAS:HDL cholesterol]
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gwas among adults residing on Korcula Island in Croatia, HDL cholesterol, the A allele associated with increased HDL cholesterol levels<br><br> [PharmGKB:Non-Curated GWAS results: Genome-wide association study of biochemical traits in Korcula Island, Croatia. (Initial Sample Size: 898 individuals; Replication Sample Size: NR); (Region: 4q13.1; Reported Gene(s): LPHN3; Risk Allele: rs4599440-A); (p-value= 0.000002).This variant is associated with Biochemical measures.] [GWAS:Biochemical measures]
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[GWAS:None]
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C allele is associated with 0.96mg/dl increase in HDL cholesterol (good cholesterol).
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[GWAS:None]
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[GWAS:None]
Frequency: 42.9%
References:18
References:18
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T allele is associated with 1.76mg/dl increase in HDL cholesterol (good cholesterol). [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 15q22.1; Reported Gene(s): LIPC; Risk Allele: rs10468017-T); (p-value= 8E-23).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
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Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Investigation of variants identified in caucasian genome-wide association studies for plasma high-density lipoprotein cholesterol and triglycerides levels in Mexican dyslipidemic study samples. Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration. [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 16q13; Reported Gene(s): CETP; Risk Allele: rs173539-T); (p-value= 4E-75).This variant is associated with HDL cholesterol.] [GWAS:HDL cholestero...
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[GWAS:HDL cholesterol]
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Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. [GWAS:None]
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A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. Genetic determinants of circulating sphingolipid concentrations in European populations. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. A single nucleotide polymorphism in the FADS1/FADS2 gene is associated with plasma lipid profiles in two genetically similar Asian ethnic groups with distinctive differences in lifestyle. Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC). Genetic variation in lipid desaturases and its impact on the development of human disease. Genetic loci associated with lipid concentrations and cardi...
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[GWAS:Systemic lupus erythematosus]
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The G allele of this SNP in the TOMM40 gene may be associated with late-onset Alzheimer's disease. Association of ApoE genetic variants with obstructive sleep apnea in children. Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. A genome-wide association study for late-onset Alzheimer's disease using DNA pooling. Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease. Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Genome-wid...
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[GWAS:None]
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per the 23andMe blog, the minor allele of this SNP (T) was associated with increased HDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} Identification of a novel risk locus for progressive supranucl...
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[PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 12q24.11; Reported Gene(s): MMAB,MVK; Risk Allele: rs2338104-C); (p-value= 0.0000000001).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol] [GWAS:HDL cholesterol]
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[GWAS:HDL cholesterol]
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[GWAS:None]
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The C allele of this SNP in the NR1H3 gene is associated with increased (but still low) risk of progressive supranuclear palsy. [PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. (Initial Sample Size: 4,763 individuals; Replication Sample Size: NR); (Region: 11p11.2; Reported Gene(s): NR1H3; Risk Allele: rs7120118-G); (p-value= 0.00000004).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
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The G allele of rs4846914 is associated with higher risk of hypertriglyceridemia. ] [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 1q42.13; Reported Gene(s): GALNT2; Risk Allele: rs4846914-G); (p-value= 0.00000004).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol] [GWAS:Triglycerides]
Frequency: 51.8%
References:1
References:1
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HDL cholesterol levels being the quantitative trait associated with in [GWAS:Quantitative traits]
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[GWAS:None]
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[GWAS:HDL cholesterol]
Frequency: 59.3%
References:1
References:1
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[GWAS:HDL cholesterol]
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[GWAS:HDL cholesterol]
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[GWAS:None]
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gwas among adults residing on Korcula Island in Croatia, HDL cholesterol, the A allele associated with decreased HDL cholesterol levels<br><br> [PharmGKB:Non-Curated GWAS results: Genome-wide association study of biochemical traits in Korcula Island, Croatia. (Initial Sample Size: 898 individuals; Replication Sample Size: NR); (Region: 12q12; Reported Gene(s): Intergenic; Risk Allele: rs871392-A); (p-value= 0.000003).This variant is associated with Biochemical measures.] [GWAS:Biochemical measures]
Frequency: 88.5%
References:1
References:1
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[GWAS:HDL cholesterol]
average
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rs1121980, a SNP in the FTO gene, showed the strongest association of several SNPs in the region with early onset obesity in a study of ~1,000 Caucasians. The odds ratio for the rs1121980(T) risk allele was 1.66 (CI: 1.37–2.01); and the odds ratios for heterozygotes and homozygotes (rs1121980(T;T)) were estimated (with a correct p<0.0001) at 1.67 (CI: 1.22–2.27) and 2.76 (CI: 1.88–4.03), respectively. Note that although rs1121980 showed the strongest association, it is in a block in the FTO gene of at least 5 other SNPs that are in linkage disequilibrium (r<sup>2</sup>>=0.88 for all). The other 5 SNPs are: * rs9939973 * rs7193144 * rs9940128 * rs8050136 * rs9939609 This SNP is also associated with (severe) obesity i...
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T allele is associated with 3.47mg/dl increase in HDL cholesterol (good cholesterol). [PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of HDL-C and apolipoprotein A1. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): HDL-C: p = 1.0 x 10 (-41);ApoA1: p = 1.1 x 10(-34). Type of association: CO; GN] [OMIM:?] [GWAS:HDL cholesterol]
common in complete genomics
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rs1800588, also known as the -514C/T polymorphism of the LIPC gene, may influence the levels of the 'good' cholestorols, the high density lipoprotein (HDL) cholesterols. Generally, the (T) allele (as published) is considered to lead to higher HDL levels. However, high HDL cholesterol, at least when combined with another HDL raising SNP (rs708272), doesn't appear to actually protect individuals from coronary artery disease, at least based on one study of ~800 Caucasian male patients. Associations between HDL-cholesterol and polymorphisms in hepatic lipase and lipoprotein lipase genes are modified by dietary fat intake in African American and White adults. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. Low-density lipoprotein and high-density lipopr...
common in complete genomics
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rs261332 increases susceptibility to Elevated HDL-Cholesterol for carriers of the A allele A allele is associated with 1.41mg/dl increase in HDL cholesterol (good cholesterol).
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[PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,815 individuals; Replication Sample Size: NR); (Region: 2p24.1; Reported Gene(s): APOB; Risk Allele: rs6754295-C); (p-value= 0.00000003).This variant is associated with Triglycerides.] [GWAS:HDL cholesterol]
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per the 23andMe blog, the minor allele of this SNP (T) was associated with decreased HDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} Analysis of recently identified dyslipidemia alleles reveals t...
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[GWAS:HDL cholesterol]
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per the 23andMe blog, the minor allele of this SNP (T) was associated with increased HDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Genome-wide association a...
Magnitude: 0
Frequency: 77.9%
Repute:Good
References:18
Frequency: 77.9%
Repute:Good
References:18
common on affy axiom data
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rs17145738 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched normolipidemic controls [PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,684 individuals; Replication Sample Size: 5,312-9,707 individuals; Risk Allele: rs17145738-C). This variant is associated with triglyceride levels.] [GWAS:Triglycerides] [GWAS:Triglycerides]
common in complete genomics
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per the 23andMe blog, the minor allele of this SNP (C) was associated with decreased HDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Common variants at 30 loc...
Magnitude: 0
Frequency: 80.5%
Repute:Good
References:13
Frequency: 80.5%
Repute:Good
References:13
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Repeatedly associated with elevated lipids according to A allele is associated with 2.09mg/dl increase in HDL cholesterol (good cholesterol). [GWAS:HDL cholesterol]
Magnitude: 0
Frequency: 80.5%
Repute:Good
References:10
Frequency: 80.5%
Repute:Good
References:10
common on affy axiom data
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G allele is associated with 2.44mg/dl increase in HDL cholesterol (good cholesterol). Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration. Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC). [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 8p21.3; Reported Gene(s): LPL; Risk Allele: rs12678919-G); (p-value= 2E-34).This variant is associated with HDL cholesterol....
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HDL cholesterol levels being the quantitative trait associated with in [GWAS:Quantitative traits]
Magnitude: 0
Frequency: 81.2%
Repute:Good
References:11
Frequency: 81.2%
Repute:Good
References:11
normal
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rs17482753 increases susceptibility to Elevated HDL-Cholesterol for carriers of the T allele rs17482753 increases susceptibility to Elevated triglycerides for carriers of the T allele [GWAS:HDL cholesterol]
common on affy axiom data
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased LDL cholesterol, increased HDL, and decreased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Cur...
common in complete genomics
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per the 23andMe blog, the minor allele of this SNP (T) was associated with decreased HDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Common variants at 30 loc...
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[GWAS:HDL cholesterol]
common in clinvar
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[PharmGKB:Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of triglycerides. Study size:6382. Study population/ethnicity: Caucasian women. Significance metric(s): P = 4.7 x 10(-11). Type of association: CO; GN] [OMIM:LIPOPROTEIN LIPASE; LPL] [GWAS:HDL cholesterol]
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The rs964184(G;G) genotype is associated with hypertriglyceridemia. [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 11q23.3; Reported Gene(s): APOA1, APOC3, APOA4, APOA5; Risk Allele: rs964184-G); (p-value= 0.000000000001).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
common in complete genomics
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[PharmGKB:Curated This SNP has been associated with small changes in HDL cholesterol levels. The C allele has been correlated with lower HDL.] [GWAS:HDL cholesterol]
64 snps
(hide) Hearing loss
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rs2227956 in HSP70-hom, resulted in a significant association with noise-induced hearing loss [PharmGKB:Curated The C allele of this SNP is part of a haplotype that has been associated with protection from hypersensitivity to carbamazepine.] [OMIM:?]
Frequency: 47.8%
References:2
References:2
References:2
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rs1043618 in HSP70-1, resulted in a significant association with noise-induced hearing loss [OMIM:?]
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This variant was associated with cisplatin-induced hearing loss from a large candidate gene screen in 2 pediatric cohorts. Study size: 166 (54 discovery, 112 replication). Study population/ethnicity: Children with neoplasms receiving cisplatin; Canada. Significance metric(s): OR = 16.89 (CI 2.27-125.88); p = 0.00022 Type of association: CO; TOX; ADR] [OMIM:?]
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23andMe blog hearing loss linked to a chemotherapy drug named Cisplatin. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This variant was associated with cisplatin-induced hearing loss from a large candidate gene screen in 2 pediatric cohorts.. Study size: 54 (discovery); 112 (replication). Study population/ethnicity: Children with neoplasms receiving cisplatin; Canada. Significance metric(s): OR = 5.52 (CI 1.91, 15.95); p = 0.000182 Type of association: CO; TOX; ADR] [OMIM:?]
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
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Hearing loss? Connexin 26-Related Nonsyndromic Sensorineural Hearing Loss see rs80338939
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Hearing loss? Connexin 26-Related Nonsyndromic Sensorineural Hearing Loss rs80338942
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
common in clinvar
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rs111033199, also known as V138F, is a SNP in the SLC26A4 gene associated with the hearing loss condition known as Pendred Syndrome. [OMIM:?]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
common in clinvar
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rs111033244, also known as E384G, is a SNP in the SLC26A4 gene associated with the hearing loss condition known as Pendred Syndrome. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs121908362, also known as H723R, is a SNP in the SLC26A4 gene associated with the hearing loss condition known as Pendred Syndrome. [OMIM:?]
18 snps
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1.5x increased risk for CAD 1.5x higher risk for coronary artery disease
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rs1333049 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is most likely (C); the odds ratio associated with heterozygotes is 1.47 (CI 1.27-1.70), and for homozygotes, 1.9 (CI 1.61-2.24). This SNP has also been reported to have the highest association of any SNP studied in a subsequent experiment conducted with the resources of the German MI [Myocardial Infarction] Family Study. The initial studies were conducted on Caucasian populations. A subsequent study of Japanese and Korean patients has also found rs1333049 to be associated with increased coronary artery disease risk, with roughly similar odds ratios. '''Further reading (with comments)''' - A long-term study of a cohort of 76...
lower risk of ischemic stroke
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rs2943634 is a SNP found to be reproducibly associated with heart disease rs2943634 associated with high density lipoprotein (HDL) cholesterol Association studies of 22 candidate SNPs with late-onset Alzheimer's disease. Evaluation of the association of genetic variants on the chromosomal loci 9p21.3, 6q25.1, and 2q36.3 with angiographically characterized coronary artery disease. Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Genome-wide association studies for atherosclerotic vascular disease and its risk factors. Genetics of coronary artery disease: focus on genome-wide association studies. Evaluation of population impact of candidate polymorphisms for coronary heart disease in the Framingham Heart Study Offspri...
higher risk of of coronary heart disease coronary heart disease
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rs662, also known as Q192R, is a SNP in the PON1 gene. It codes for amino acid 192 of the paraoxonase (PON) protein. Variants of this SNP affect PON catalytic efficiency and are correlated with Heart disease and trait-anxiety scores. The normal form, rs662(A), encodes a glutamine (Q), while the variant, rs662(G)), encodes an arginine (R). . While some populations show an association between this SNP and Heart disease, not all do. Perhaps the most striking finding was reported in Japanese patients with non-insulin dependent diabetes mellitus (NIDDM). NIDDM patients with either one or two rs662(G) alleles had a 9 fold higher risk of coronary heart disease compared with rs662(A;A) NIDDM patients. table of odds for cardiovascular disease outcomes 274 ovarian epithelial carcinoma cases and 452 ...
No benefit to alcohol consumption
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rs708272, also known as the TaqIB polymorphism of the CETP gene, may influence the levels of the 'good' cholesterols, the high density lipoprotein (HDL) cholesterols. Generally, the B2 allele is considered to lead to higher HDL levels. However, high HDL cholesterol, at least when combined with another HDL raising SNP (rs1800588), doesn't appear to actually protect individuals from coronary artery disease, at least based on one study of ~800 Caucasian male patients. A similarly confusing picture emerges from a study of two populations of 10,000+ individuals each. The distribution of the CETP genotype was observed to be different in population-based studies compared with studies in populations selected by high cardiovascular risk, and contradictory results were seen when trying to figure out...
MI risk, aspirin resistance 23andMe blog lower odds of early stent thrombosis
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The 'A2' allele of the platelet specific alloantigen system is encoded by rs5918(C), and it has been implicated as increasing the risk of myocardial infarctions, heart disease, and resistance to blood-thinning benefits of aspirin. On its own, the A2 allele is implicated especially in early onset heart disease ; in combination with the 4G allele of the PAI1 gene, rs1799889, the increased risk of myocardial infarction in a Finnish study population was 4 fold higher (odds ratio = 4.5, p=0.001), particularly in males (odds ratio = 6.4, p=0.0005) . Olympic skater Sergei Grinkov, who had this risk factor, died of a heart attack at age 28. A2 allele carriers also appear to be relatively resistant to the anti-thrombotic (i.e. anti-clotting) actions normally associated with aspirin] use. A protecti...
1.3x increased risk for heart disease
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rs5174 encodes a variant of the LRP8 gene, encoding the low density lipoprotein receptor-related 8 protein (or the apolipoprotein e receptor). The variant affects the protein, changing an arginine to a glutamine; depending on the publication, it can be referred to by terms like R952Q or Arg952Gln. In three Caucasian populations combined, the odds ratio for coronary artery disease or myocardial infarction (and thus heart disease) is 1.31 (adjusted p=0.0003). Note that this association was only seen in populations with familial and premature disease, as a study of 1,231 patients with primarily late-onset, sporadic heart disease did not show any correlation with this SNP. rs5174 (or its equivalent, rs5177) was analyzed in 1,210 patients with familial MI and 1,015 controls from the German MI F...
1.8x increased risk for high blood pressure
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rs4961 is a variation in the adducin 1 ADD1 gene, encoding a change from a glycine to a tryptophan, so it is also known as G460W or Gly460Trp. Originally, a study of 477 Italian patients indicated that carriers of one or two rs4961(T) alleles were at 1.8x increased risk for hypertension (CI: 1.32-2.43). This study also indicated that carriers of the risk (T) allele responded better to diuretics and sodium-restricted diets, in that they tended to lower their blood pressure by ~10 mmHg points compared to rs4961(G;G) homozygotes similarly treated. Subsequent studies have tended to confirm this association, and to extend it to risk for heart disease. They also have tended to confirm that risk allele carriers respond better to therapy. In a study of ~2200 Belgian patients, rs4961(T) carriers we...
increased risk of coronary heart disease; better response to statins
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rs2298566 is a SNP in the SNX19 gene. The risk allele in terms of heart disease is rs2298566(C). This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 possible risk variants (two copies of each of the five SNPs) were assigned a GRS of 5 and those carrying no risk variants a GRS of -5. A high GRS was defined as 3 or higher. Approximately 4% of the white cohort in ARIC...
Magnitude: 2
Frequency: 42.9%
Repute:Bad
References:8
Frequency: 42.9%
Repute:Bad
References:8
1.26x increased risk for heart disease
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rs17228212 is a SNP found to be associated with heart disease by the German MI (Myocardial infarction) Family Study group in two populations. The odds ratio per allele is 1.26 (CI: 1.11-1.44, p=0.0178). rs599839, rs4970834 and rs17228212 associated with non-HDL cholesterol
Magnitude: 2
Frequency: 50.0%
Repute:Bad
References:77
Frequency: 50.0%
Repute:Bad
References:77
1.3x risk for Heart Attack. Normal risk for Abdominal Aortic Aneurysm and Brain Aneurysm. One copy of an SNP that increases risk of Myocardial Infarction (Heart Attack) and other Coronary Heart Disease. It has been shown that regularly eating raw vegetables and fruit can reduce the risk to the same level as people without this SNP. This SNP also has the normal medium risk of abdominal aortic aneurysm (weakened artery to abdomen and legs) or brain aneurysm (weakened artery to brain).
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This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...
increased risk for heart disease
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discussed in this blog post as possibly playing a role in coronary heart disease This SNP was also associated with increased risk for coronary artery disease in a Korean population. The association remained significant after adjusting for significant clinical covariates (P=0.001 to 0.024). We identified one risk haplotype (GGGG; P=0.017) and one protective haplotype (AAAA; P=0.007) for development of CAD. Further analysis suggested that the SNPs probably confer susceptibility to CAD in a dominance model (covariates-adjusted P=0.001 to 0.024; OR=2.37 to 1.54). Also found to be significant in a study of 416 Italian myocardial infarction patients. Found to be associated with coronary heart disease in a study of 1360 Chinese Han patients, with an odds ratio of 1.52 (CI: 1.13 - 2.04) for rs2383...
1.4x increased risk for heart disease
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rs10757274 and rs2383206 can significantly increase the risk of heart diseaseAbout one in every four Caucasians are thought to carry the variants, and their risk of coronary heart disease is increased by 30 to 40%. rs10757278] in the same region has been linked to diabetes The chromosomal region where these SNPs are located is 9p21, and has no known genes. a [http://suicyte.wordpress.com/2007/05/26/soul-searching-i/ blog post about investigating rs10757274 and rs2383206 This SNP was also associated with increased risk for coronary artery disease in a Korean population. Also found to be significant in a study of 416 Italian myocardial infarction patients. A study of 1,000+ patients with early-onset angiographic coronary artery disease (CAD) concluded that rs2383206(G) was associated with an...
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
1.9x risk 1.9x higher risk for coronary artery disease
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rs383830 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.60 (CI 1.16-2.21), and for homozygotes, 1.92 (CI 1.40-2.63).
hypertension increases risk 3.75x for sudden cardiac death
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rs187238, also known as -137 G/C, is a SNP in the interleukin 18 IL18 gene. Based on studying autopsies of 700 men in the Helsinki Sudden Death Study, there was a significant interaction between IL-18 genotype and hypertension impacting on the risk of sudden cardiac death (SCD) due to coronary heart disease (CHD). Among rs187238(G;G) homozygotes, hypertension was a major risk factor for SCD due to CHD (adjusted odds ratio 3.75, CI:1.78-7.91, p < 0.001) and hypertension also associated with larger coronary atherosclerotic plaque areas (p = 0.002) and the occurrence of complicated plaques (adjusted OR 8.38, CI: 2.39-29.33, p < 0.001). Among rs187238(C) allele carriers, hypertension was not a significant risk factor for CHD-related SCD or CAD and did not associate with the development o...
common, but 2.2x higher risk for heart disease
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rs8055236 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.91 (CI 1.33-2.74), and for homozygotes, 2.23 (CI 1.56-3.17). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,926 cases, 2,938 controls; Replication Sample Size: (see Samani 2007); Risk Allele: rs8055236-G). This variant is associated with coronary disease.] [GWAS:Coronary disease]
Magnitude: 1.4
Frequency: 22.3%
Repute:Good
References:4
Frequency: 22.3%
Repute:Good
References:4
Reduced risk (0.7x) for heart disease Reduced risk (0.7x) for heart disease
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rs17672135 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 0.70 (CI 0.61-0.81), and for homozygotes, 1.32 (CI 0.79-2.22). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,926 cases, 2,938 controls; Replication Sample Size: (see Samani 2007); Risk Allele: rs17672135-C). This variant is associated with coronary disease.] [GWAS:Coronary disease]
Magnitude: 1.34
Frequency: 50.0%
Repute:Bad
References:18
Frequency: 50.0%
Repute:Bad
References:18
1.34x higher risk for myocardial infarction
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rs17465637 is a SNP found to be associated with heart disease by the German MI (Myocardial infarction) Family Study group This 2011 study concluded that the only MIA3 gene SNP to be associated with increased risk for myocardial infarction is rs17465637, with an odds ratio of 1.17 (CI: 1.04-1.32) and 1.37 (CI: 1.08-1.74) for carriers of one or two (C) alleles, respectively. 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 con...
1.3x increased risk for heart disease
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rs501120 is a SNP found to be associated with heart disease in two populations by the German MI (Myocardial infarction) Family Study group. The risk allele in dbSNP orientation is rs501120(A). The odds ratio per allele is 1.33 (CI: 1.20-1.48, adjusted p=0.0248). Association of genetic variants and incident coronary heart disease in multiethnic cohorts: the PAGE study. Comparative analysis of genome-wide association studies signals for lipids, diabetes, and coronary heart disease: Cardiovascular Biomarker Genetics Collaboration. Genetic risk score and risk of myocardial infarction in Hispanics. |OA=1 }} Coronary artery disease-related genetic variant on chromosome 10q11 is associated with carotid intima-media thickness and atherosclerosis. Genetics and cardiovascular disease: Design and dev...
complex! see rs4880
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The rs4880(T) allele, part of the codon for amino acid valine at codon 16 of the antioxidant protein from the mitochrondrial superoxide dismutase 2 SOD2 gene, is the most common in most populations studied. The rs4880(C) allele gives rise to an alanine at this position is it also known as Val16Ala manganese superoxide dismutase, or A16V. There appears to be some conflict in the literature over the effect of this SNP. Having a valine at codon 16 is said to reduce enzyme activity , and thus lead to increased oxidative stress, yet in at least one study of the actual enzyme levels measured in people, SOD2 activity was 33% higher in (C;T) or (T;T) individuals compared to (C;C) individuals . Regardless of how this resolves, several phenotypic associations have been reported for this SNP, includi...
slightly increased heart attack risk
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rs8089, a SNP in the thrombospondin-2 THBS2 gene, was studied as part of a large study (>5,000 Caucasian patients) for risk of myocardial infarction and thus heart disease. Although statistically not overwhelming, a risk was seen (odds ratio 1.19, CI: 1.02-1.39, compared to (T;T) homozygotes) for carriers of the less common rs8089(G) allele. In a meta-analysis combining several studies, no statistically significant association for heart attacks was seen for rs8089, nor for that matter, 2 other SNPs, rs2228262 (also known as Asn700Ser) or rs1866389 (also known as Ala387Pro), in thrombospondins -1 and -4, respectively. A functional polymorphism in THBS2 that affects alternative splicing and MMP binding is associated with lumbar-disc herniation. An association study of thrombospondin 1 and...
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SNP rs752658 has been associated with both cholesterol levels and low-density lipoprotein levels in the Framingham Heart Study datasets, and is thus associated with heart disease. source
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SNP rs287354 has been associated with both cholesterol levels and low-density lipoprotein levels in the Framingham Heart Study datasets, and is thus associated with heart disease. source A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study.
normal
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rs7439293 is a SNP in the PALLD gene. The risk allele in terms of heart disease is rs7439293(A). This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 possible risk variants (two copies of each of the five SNPs) were assigned a GRS of 5 and those carrying no risk variants a GRS of -5. A high GRS was defined as 3 or higher. Approximately 4% of the white cohort in ARIC...
1.48x risk
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rs1048990, also known as the exon-1 -8C/G SNP in the PSMA6 gene, has been reported in a large study of Japanese patients to be associated with increased risk for myocardial infarction (heart disease). The risk allele (oriented to the dbSNP entry) is (G). The odds ratio (based on an additive model) is 1.48 (CI 1.23-1.77, p = 1.2 x 10e-5). given the rarity of this variant in Caucasians, the attributable risk of rs1048990 for MI is unlikely to be great in western populations Various ways of calculating the association between rs1048990 and myocardial infarction all led to odds ratios of around 1.2 - 1.5 in a case-control association study on a cohort of 1,884 MI patients and 2,643 unrelated controls from the Chinese population. [OMIM:PROTEASOME SUBUNIT, ALPHA-TYPE, 6; PSMA6]
normal risk
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rs5065, also known as T2238C, is a SNP in the atrial natriuretic precursor A NPPA gene. A large study has been conducted in which 42,418 hypertensive participants 55 or older were followed for several years while on one of four medications: a diuretic, a calcium antagonist, an angiotensin-converting enzyme inhibitor, or an alpha-blocker. The primary endpoint was either fatal heart disease or a heart attack. The blood pressure after six months of rs5065(G;G) patients (note: genotype is in dbSNP orientation, not as published) was lower if the patients were treated with diuretics compared to other medications, with smaller variation seen for (A;A) genotypes. The authors noted that none of the findings retained statistical significance after correction for multiple comparisons, but since the t...
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rs1171381, a SNP in the FAM5C gene, has been associated with both high-density lipoprotein levels and triglyceride levels in the Framingham Heart Study datasets, and is thus associated with heart disease. source
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rs815160, a SNP in the FAM5C gene, has been associated with both high-density lipoprotein levels and triglyceride levels in the Framingham Heart Study datasets, and is thus associated with heart disease. source
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SNP rs2827196 has been associated with both diastolic blood pressure and systolic blood pressure in the Framingham Heart Study datasets, and is thus associated with high blood pressure and heart disease. source
1.2x risk
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rs6922269 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.17 (CI 1.04-1.32), and for homozygotes, 1.65 (CI 1.32-2.06). [PharmGKB:Non-Curated GWAS Results: Genomewide association analysis of coronary artery disease (Initial Sample Size: 1,926 cases, 2,938 controls; Replication Sample Size: 875 cases, 1,644 controls; Risk Allele: rs6922269-A).] [GWAS:Coronary disease]
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rs20455, often called Arg719 or 719Arg, is a reasonably well studied SNP in the KIF6 gene. The risk allele (encoding the arginine at position 719) is rs20455(C). An extensive 2010 meta-analysis, including over 17,000 patients, suggests this variant does not significantly influence coronary artery disease risk. This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 pos...
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SNP rs39317 has been associated with both cholesterol levels and low-density lipoprotein levels in the Framingham Heart Study datasets, and is thus associated with heart disease. source
common; higher LDL-C and total cholesterol
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rs174537 is a SNP near the FADS1 gene on chromosome 11. The FADS1 gene is one of 3 fatty acid desaturases in this region; higher polyunsaturated fatty acids (PUFA) levels are generally correlated with lower risk for heart disease. A study of 1,075 participants in the InCHIANTI study on aging concluded that rs174537(T;T) individuals had lower arachidonic acid (AA), as well as lower levels of all other polyunsaturates measured (excepting linoleic acid, which followed the opposite pattern, and alpha-linoleic acid), compared to (G;G) homozgyotes (p = 6 x 10e-46), and that this one SNP accounted for almost 19% of the variance in AA levels. Individuals carrying at least one rs174537(G) allele had higher low-density lipoprotein (LDL-C) and total cholesterol levels. This effect of rs174537 was con...
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This paper implicates this snp as playing a role in heart disease. Having a C at this position is considered normal. Having a T at this position increases the risk of heart disease. Approximate 27% of people carry this risky form.
1.75x risk of MI
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This SNP, located on chromosome 2 in a gene (VAMP8) associated with platelet activation, may be associated with early onset myocardial infarction (MI). The risk allele for this SNP (in dbSNP orientation) is rs1010(G), with an odds ratio of 1.75 (CI: 1.17–2.62). Furthermore, this SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 possible risk variant...
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SNP rs1550922 has been associated with both glucose levels and body-mass index (eg obesity) in the Framingham Heart Study datasets, and is thus associated with heart disease. source
1.29x increased risk for heart disease
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rs599839 is a SNP found to be associated with heart disease by the German MI (Myocardial infarction) Family Study group, over several populations. The odds ratio for the (common) risk allele, rs599839(A), is 1.29 (CI: 1.18-1.40, adjusted p=0.0006). rs599839 and rs4970834 explain about 1% of the variation in circulating LDL-cholesterol levels. 'When we look at this particular genetic variance, of all the cholesterol variation among the population, 1% of it can be attributed to this particular locus,' said Sandhu. 'This is equivalent to more established genes for LDL regulation, particularly APOE.' Another study also reports an association between rs599839(A) and higher LDL levels, in over 4,000 Caucasian Europeans. In one study, the (A) allele is associated with a 6% increase in nonfasting ...
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SNP rs966376 has been associated with both cholesterol levels and high-density lipoprotein levels in the Framingham Heart Study datasets, and is thus associated with heart disease. source
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SNP rs2286983 has been associated with both cholesterol levels and body-mass index (eg obesity) in the Framingham Heart Study datasets, and is thus associated with heart disease. source
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G-C-T-C haplotype of rs2340690-rs788016-rs2305560-rs2565163 has odds ratio of 1.91 (CI: 1.26-2.89, p=0.002) for coronary heart disease compared to G-T-T-C, based on a study of 1,000 Han Chinese patients and matched controls. * Note: Haplotype allele assignments may not be in dbSNP orientation.
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rs2331291 a non-coding RNA, MIAT, that confers risk of Myocardial infarction.
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,AEHA 2008 ppt - rs4404477(A)/rs1676232(A) defines a significant left main coronary artery disease risk haplotype
Repute:Bad
References:38
References:38
~1.2x increased risk for heart disease
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rs10757274 is a SNP located in chromosomal region 9p21; to date (2009), it is the strongest genetic predictor of early myocardial infarction (heart attack) discovered so far. SNPs in this region are also associated with increased risk of stroke, abdominal aortic aneurysm (AAA), and intracranial aneurysm. Based on a large (20,000+) study primarily of Caucasian females, it appears that on its own, this single SNP does not improve on the discrimination or classification of predicted heart disease risk achieved by traditional risk factors, high-sensitivity C-reactive protein, and a family history of premature myocardial infarction. rs10757274 and rs2383206 can double the risk of heart diseaseAbout one in every four Caucasians are thought to carry the gene variants. rs10757278] in the same regi...
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rs1800787(T;T) homozygotes are at 6 fold higher risk compared to (C;C) homozygotes or (C;T) heterozygotes for carotid atherosclerosis . This polymorphism is known as the 'C148-T' variant, and is located in at the '-148' position of the FGB gene, also known as beta fibrinogen. A meta-analysis of 7 studies did not find a significant association between the -148C/T FGB SNP and susceptibility to coronary artery disease in Chinese populations. Note: due to inconsistencies between databases and the literature, the association of this rs# with this polymorphism name as published is highly likely but not guaranteed.
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SNP rs287474 has been associated with both cholesterol levels and low-density lipoprotein levels in the Framingham Heart Study datasets, and is thus associated with heart disease. source
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
normal fat metabolism; common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
normal
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rs7250581 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.06 (CI 0.79-1.43), and for homozygotes, 1.40 (CI 1.05-1.86).
normal risk
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rs5082 is a SNP in the apolipoprotein APOA2 gene, and may influence obesity and heart disease risk. Individuals homozygous for the -265T>C polymorphism in rs5082, i.e. individuals with the rs5082(C;C) genotype of the Apolipoprotein A-II gene (APOA2) promoter, are associated with increased Body Mass Index and food intake in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Study of ~1000 individuals. The odds ratio for obesity in (C;C) individuals compared to rs5082(T) allele carriers was 1.70 (CI: 1.02-2.80, p=0.039). Total energy, total fat, and total protein intake were all significantly higher in (C;C) individuals. In a separate study, a case-control analysis of 484 Australian male coronary artery disease patients concluded that rs5082(C;C) individuals were at significant...
normal risk
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rs1024611, also known as the -2578A>G SNP due to its position in the promoter of the monocyte chemoattractant protein-1 MCP-1 CCL2 gene, influences the production of its corresponding protein, a chemokine involved in inflammatory responses. In a study focusing on 679 apparently healthy siblings of people with premature heart disease, investigators found that carriers of an rs1024611(C) allele - oriented as in dbSNP, not as published - independently predicted the risk of exercise induced ischemia in general. The odds ratio was reported to be 1.86 (CI: 1.14-3.04, p=0.014), regardless of race, age, sex and other factors. However, it is not clear if this risk carries over to individuals who lack siblings with heart disease. discussed in the 23andMe blog as being relevant to HIV rs1024611 is...
normal
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rs3900940 is a SNP in the MYH15 gene. The risk allele in terms of heart disease is rs3900940(C). This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 possible risk variants (two copies of each of the five SNPs) were assigned a GRS of 5 and those carrying no risk variants a GRS of -5. A high GRS was defined as 3 or higher. Approximately 4% of the white cohort in ARIC...
normal
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rs688034 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.11 (CI 0.98-1.25), and for homozygotes, 1.62 (CI 1.34-1.95). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,926 cases, 2,938 controls; Replication Sample Size: (see Samani 2007); Risk Allele: rs688034-T). This variant is associated with coronary disease.] [GWAS:Coronary disease]
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G-C-T-C haplotype of rs2340690-rs788016-rs2305560-rs2565163 has odds ratio of 1.91 (CI: 1.26-2.89, p=0.002) for coronary heart disease compared to G-T-T-C, based on a study of 1,000 Han Chinese patients and matched controls. * Note: Haplotype allele assignments may not be in dbSNP orientation.
Normal/Average risk for Alzheimer's
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Apolipoprotein E ApoE status is technically defined by two different SNPs, rs429358 and rs7412. This SNP, rs4420638, is situated about 14kb away in the adjacent ApoC1 gene and is co-inherited with ApoE and thus associated with late-onset Alzheimer's disease. rs4420638 (the proxy SNP) is not independent of rs429358. These two SNPs are correlated with each other and it's believed that most of the association with AD at rs4420638 is due to its proximity to rs429358. That said, rs4420638 is not a perfect proxy for rs429358 either -- rs4420638 correlates better for certain genotypes and for certain ethnicities. For example, if you have the genotype at rs4420638 that is more correlated with the e4 allele of APOE, you still only have a 50% chance of actually having the e4 allele. And rs4420638 is...
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y or Cys282Tyr mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who act...
Magnitude: 0
Frequency: 93.8%
Repute:Good
References:0
Frequency: 93.8%
Repute:Good
References:0
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rs10489535, a SNP in the ACOT7 gene, has been associated with both cholesterol levels and triglyceride levels in the Framingham Heart Study datasets, and is thus associated with heart disease. source
Magnitude: 0
Frequency: 93.8%
Repute:Good
References:1
Frequency: 93.8%
Repute:Good
References:1
common in complete genomics
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SNP rs10510468 has been associated with both very-low density lipoprotein levels and high-density lipoprotein levels in the Framingham Heart Study datasets, and is thus associated with heart disease. source
normal
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rs4986790, a SNP also known as Asp299Gly (and also 896A/G) in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in th...
normal
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rs4986791, a SNP also known as Thr399Ile (and also 1196C/T) in the TLR4 gene, is often studied along with a cosegregating SNP known as Asp299Gly, rs4986790. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986791 is (T). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in t...
normal
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rs662799 is a SNP in the APOA5 gene. The rarer rs662799(C) allele has been associated in multiple reports (cited below) to be associated with higher triglyceride levels. Independently of triglyceride levels, perhaps, a study based on 1,864 Italian patients <45 years old at the time of their first heart attack (myocardial infarction) concluded that this SNP is associated with higher risk for an early heart attack, with a per C allele odds ratio of 1.44 (CI: 1.23-1.69, p = 6.7 × 10(-5)). This SNP has also been reported to help prevent weight gain from high fat diets. 1,073 men and 1,207 women participating in the Framingham Offspring Study rs662799 -1131T>C in modulates the effect of fat intake on BMI and obesity risk in both men and women. Individuals with at least one C allele g...
common in clinvar
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rs268, also known as LPL '''Asn291Ser''' as well as '''LPL N291S''' or '''N318S''', a SNP in the lipoprotein lipase LPL gene, has been linked to increased susceptibility to hypertriglyceridemia, heart disease, Type-2 diabetes, idiopathic venous thromboembolism. A systematic review and meta-analysis of the relationship between lipoprotein lipase Asn291Ser variant and diseases. The summary standardized mean difference (SMD) of plasma triglyceride (TG) for carriers compared with noncarriers of the Asn291Ser variant was 3.23 (P < 0.00001). The summary SMD of plasma HDL-cholsterol (HDL-C) for carriers compared with noncarriers of the Asn291Ser variant was -3.42 (P < 0.0001). The summary SMD of the association of the Asn291Ser variant with plasma TG increased with increasing age and weight...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal risk
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rs34210653 is a SNP in the ALOX15 gene, either encoding a threonine or a methionine at position 560 of the corresponding protein. This SNP is also known as T560M; the more common (C) allele encodes the threonine, and the rarer (T) allele encodes the methionine. In mice, this protein appears to promote atherosclerosis, and mice completely lacking the entire gene are free of atherosclerosis. In contrast, rs34210653(T;T) humans, who effectively have a non-functioning variant, do not show a statistically significant decreased risk for coronary artery disease. And rs34210653(C;T) heterozygotes an increased risk of heart disease (adjusted odds ratio 1.62, p=0.02).
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Category:needs help Category:interestingThis paper implicates this snp as playing a role in heart disease. Having a G at this position is considered normal. Having an A at this position reduces the risk of heart disease. Approximate 15% of all people carry this allele. '''Technical note:''' This applies to many other snps, but here is the first clean case I've encountered. dbsnp shows ss3839 and ss16241517 are being read 'fwd' ss16940640 and ss44449258 are being read in 'rev'. This has C/T alleles when read forward, and A/G when read in reverse. Since the authors of the paper above describe this as an A/G snp, it seems they are reading in reverse. Often papers include even less information, and can leave some ambiguity about these important details. GATA2 is associated with familial early-...
common
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This SNP, located in the fourth exon of the ApoE gene, affects the amino acid at position 130 of the resulting protein. The more common rs429358 allele is (T). If the allele is (C) and the same chromosome also harbors the rs7412(C) allele, the combination is known as an APOE-ε4 allele. The APOE-ε4 allele has a strong influence on the risk of Alzheimer's disease. Both deCODEme and 23andMe (v3 chip) test for this SNP. Many studies have estimated the level of risk, and it varies depending on age, sex, ethnicity, and other factors. One meta-analysis estimated the odds ratios for homozygous rs429358(C;C) individuals compared to the more common ApoE3/ApoE3 homozygotes to be 12x for late-onset Alzheimer's and 61x for early-onset disease. Meta-analyses have also supported the association between t...
common on affy axiom data appears to be common on the 23andMe platform
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Rs3135506 (also known as S19W) is associated with severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched normolipidemic controls. It is discussed in ; however, the SNP that prevents weight gain from high fat diets is rs662799. [PharmGKB:Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of triglycerides and apolipoprotein B. Study size:6382. Study population/ethnicity: Caucasian women. Significance metric(s): triglycerides: p = 5.5 x 10(-12); ApoB: p = 8.4 x 10(-8). Type of association: CO; GN] [OMIM:?]
normal
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rs10498345 is a SNP on chromosome 14 that has been associated with coronary spasm (often a precursor to various types of heart disease) in a study of Japanese women. For unknown reasons, the prevalence of coronary spasm in higher in Japanese than in Caucasians. In this study of ~800 Japanese individuals, the ~200 women with coronary spasm were found to preferentially harbor the genotype with rs10498345(T), or to put it another way, the rs10498345(A) allele appears to be protective, with an odds ratio of 0.5 (p=3.5x10e-4). No association was seen in males. [PharmGKB:Non-Curated GWAS Results: A novel genetic marker for coronary spasm in women from a genome-wide single nucleotide polymorphism analysis (Initial Sample Size: 50 Japanese cases, 50 Japanese controls; Replication Sample Size: 151...
66 snps
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~0.8cm taller
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nature SNP rs1042725 is associated with height (P = 4E-8) in a study involving over 20,000 individuals. The gene harboring this SNP, HMGA2, is a strong biological candidate for having an influence on height, since rare, severe mutations in this gene are known to alter body size in mice and humans. rs1042725 is estimated to explain approx 0.3% of population variation in height in both adults and children (approx 0.4 cm increased adult height per C allele). rs1042725 is associated with increased height (0.36 cm 95% IC[0.12-0.61] per C allele, P=0.004). in men rs1042725 may explain 3% of height variability [PharmGKB:Non-Curated GWAS Results: A common variant of HMGA2 is associated with adult and childhood height in the general population (Initial Sample Size: 4,921 individuals; Replication S...
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[GWAS:Height]
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[GWAS:Height]
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A study of 1153 elderly Swedish men (age 70) concluded that rs2179922(G;G) homozygotes were between 0.90 - 2.3cm taller on average than either (A;G) or (A;A) genotypes. [No such association with height was seen for females.]
Frequency: 7.7%
References:1
References:1
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[GWAS:Height]
Frequency: 8.9%
References:1
References:1
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[GWAS:Height]
Frequency: 9.2%
References:2
References:2
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[GWAS:Height]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. (Initial Sample Size: 32,387 individuals; Replication Sample Size: 59,092 individuals); (Region: 20p12.3; Reported Gene(s): BMP2; Risk Allele: rs2145270-T); (p-value= 0.000006).This variant is associated with Body mass index.] [GWAS:Body mass index]
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[GWAS:Height]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 8q12.1; Reported Gene(s): PLAG1); (p-value= 0.000005).This variant is associated with Height.] [GWAS:Height]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 4p15.32; Reported Gene(s): LCORL; Risk Allele: rs6830062-?); (p-value= 0.000000005).This variant is associated with Height.] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 13; STQTL13] [GWAS:Height]
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[GWAS:Height]
Frequency: 20.4%
References:6
References:6
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[PharmGKB:Non-Curated GWAS Results: Genome-wide association analysis identifies 20 loci that influence adult height (Initial Sample Size: 13,665 individuals; Replication Sample Size: 16,482 individuals).] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 13; STQTL13] [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
Frequency: 21.2%
References:3
References:3
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
Frequency: 23.1%
References:2
References:2
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[PharmGKB:Non-Curated GWAS Results: Common variants in the GDF5-UQCC region are associated with variation in human height (Initial Sample Size: 6,669 individuals; Replication Sample Size: 28,801 individuals).] [GWAS:Height]
Frequency: 25.5%
References:1
References:1
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[GWAS:Height]
Frequency: 25.9%
References:6
References:6
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[GWAS:Height]
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[GWAS:None]
Frequency: 27.4%
References:2
References:2
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Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. [PharmGKB:Non-Curated GWAS Results: Many sequence variants affecting diversity of adult human height (Initial Sample Size: 30,968 individuals; Replication Sample Size: 8,541 individuals).] [GWAS:Height]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 12q14.3; Reported Gene(s): HMGA2; Risk Allele: rs8756-?); (p-value= 0.00000000000005).This variant is associated with Height.] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 9; STQTL9] [GWAS:Height]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 13q14.3; Reported Gene(s): DLEU7); (p-value= 0.0000000004).This variant is associated with Height.] [OMIM:?] [GWAS:Height]
Frequency: 31.0%
References:1
References:1
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[GWAS:Height]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 7q21.2; Reported Gene(s): CDK6); (p-value= 0.00000001).This variant is associated with Height.] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 11; STQTL11] [GWAS:Height] [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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23andMe blog rs314276 or the equivalent rs314263(T) yields *Female **menarche about six weeks earlier **1.2x accelerated breast development and a faster rate of increase in height and weight. **a reduction in adult height of about 0.15 inches. *Male **1.26 greater odds of advanced voice breaking at age 15 **1.19 times greater odds of advanced pubic hair at age 13 **faster rate of growth at age 10 and about a tenth of an inch less in adult height. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. [OMIM:?]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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23andMe blog rs314276 or the equivalent rs314263(T) yields *Female **menarche about six weeks earlier **1.2x accelerated breast development and a faster rate of increase in height and weight. **a reduction in adult height of about 0.15 inches. *Male **1.26 greater odds of advanced voice breaking at age 15 **1.19 times greater odds of advanced pubic hair at age 13 **faster rate of growth at age 10 and about a tenth of an inch less in adult height. [OMIM:?] [GWAS:Menarche (age at onset)]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 7p15.1; Reported Gene(s): JAZF1; Risk Allele: rs849141-?); (p-value= 0.00000000003).This variant is associated with Height.] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 17; STQTL17] [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
Frequency: 36.3%
References:5
References:5
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 5p13.3; Reported Gene(s): NPR3); (p-value= 0.0000003).This variant is associated with Height.] [OMIM:?] [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
Frequency: 36.4%
References:1
References:1
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[GWAS:Height]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS Results: Identification of ten loci associated with height highlights new biological pathways in human growth (Initial Sample Size: 15,821 individuals; Replication Sample Size: 13,671 individuals).] [OMIM:STATURE AS A QUANTITATIVE TRAIT] [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
Frequency: 38.9%
References:2
References:2
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Pubertal anthropometrics]
Frequency: 40.7%
References:1
References:1
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. [PharmGKB:Non-Curated GWAS Results: Many sequence variants affecting diversity of adult human height (Initial Sample Size: 30,968 individuals; Replication Sample Size: 8,541 individuals).] [OMIM:STATURE AS A QUANTITATIVE TRAIT] [GWAS:Height]
Frequency: 42.5%
References:3
References:3
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[GWAS:Height]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 6q24.1; Reported Gene(s): GPR126); (p-value= 0.00000000004).This variant is associated with Height.] [OMIM:STATURE AS A QUANTITATIVE TRAIT] [GWAS:Height]
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[GWAS:Height]
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Height
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[GWAS:Height]
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[GWAS:Height]
Frequency: 43.4%
References:1
References:1
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[GWAS:Height]
Frequency: 43.4%
References:1
References:1
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[GWAS:Height]
Frequency: 43.4%
References:1
References:1
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 7p22.2; Reported Gene(s): GNA12; Risk Allele: rs1182188-?); (p-value= 0.000000003).This variant is associated with Height.] [GWAS:Height]
Frequency: 43.8%
References:4
References:4
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[GWAS:Height]
Frequency: 44.1%
References:2
References:2
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[GWAS:Height]
Frequency: 44.2%
References:1
References:1
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[GWAS:Height]
Frequency: 44.2%
References:4
References:4
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 15q25.2; Reported Gene(s): ADAMTSL3); (p-value= 0.00000003).This variant is associated with Height.] [GWAS:Height]
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[GWAS:Height]
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23andMe blog *rs1867138(T;T) or rs1867137(G;G) were approximately one inch taller than rs1867138(C;C) *rs9834312(G;G) or rs939882(G;G) increased height
taller
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rs9834312 is a SNP in the filamin B, beta (actin binding protein 278) FLNB gene. Based on a study of 1,000+ Caucasians and 2,000+ Chinese, rs9834312 was associated with height in both Caucasian populations (p=0.008) and Chinese populations (p=0.017) 23andMe blog *rs1867138(T;T) or rs1867137(G;G) were approximately one inch taller than rs1867138(C;C) *rs9834312(G;G) or rs939882(G;G) increased height [OMIM:?]
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[PharmGKB:Non-Curated GWAS results: Common variants in the JAZF1 gene associated with height identified by linkage and genome-wide association analysis. (Initial Sample Size: 3,925 individuals; Replication Sample Size: 38,091 individuals); (Region: 7p15.1; Reported Gene(s): JAZF1; Risk Allele: rs1635852-A); (p-value= 0.0000000009).This variant is associated with Height.] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 17; STQTL17] [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS Results: Genome-wide association analysis identifies 20 loci that influence adult height (Initial Sample Size: 13,665 individuals; Replication Sample Size: 16,482 individuals).] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 14; STQTL14] [GWAS:Height]
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[GWAS:Height]
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Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study. [PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 6p21.33; Reported Gene(s): AIF1, NCR3; Risk Allele: rs2844479-T); (p-value= 0.00000002).This variant is associated with Weight.] [GWAS:Weight]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 20q11.22; Reported Gene(s): UQCC); (p-value= 0.0000000000001).This variant is associated with Height.] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 14; STQTL14] [GWAS:Height]
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[GWAS:Height]
Frequency: 46.0%
References:4
References:4
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[GWAS:Height]
Frequency: 46.0%
References:1
References:1
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Assessing the impact of global versus local ancestry in association studies. [GWAS:Height]
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[PharmGKB:Non-Curated GWAS Results: Genome-wide association analysis identifies 20 loci that influence adult height (Initial Sample Size: 13,665 individuals; Replication Sample Size: 16,482 individuals).] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 10; STQTL10] [GWAS:None] [GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 3q23; Reported Gene(s): ZBTB38); (p-value= 0.000000000003).This variant is associated with Height.] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 10; STQTL10] [GWAS:Height] [GWAS:Height]
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Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. Transferability and fine-mapping of genome-wide associated loci for adult height across human populations. [PharmGKB:Non-Curated GWAS Results: Identification of ten loci associated with height highlights new biological pathways in human growth (Initial Sample Size: 15,821 individuals; Replication Sample Size: 13,671 individuals).] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 10; STQTL10] [GWAS:Height] [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. [GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 9p13.3; Reported Gene(s): WDR40A); (p-value= 0.000002).This variant is associated with Height.] [GWAS:Height]
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Genome-wide association study identifies two novel loci containing FLNB and SBF2 genes underlying stature variation. [PharmGKB:Non-Curated GWAS Results: Identification of ten loci associated with height highlights new biological pathways in human growth (Initial Sample Size: 15,821 individuals; Replication Sample Size: 13,671 individuals).] [GWAS:Height]
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[GWAS:Height]
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[OMIM:STATURE QUANTITATIVE TRAIT LOCUS 11; STQTL11] [GWAS:Height]
Frequency: 47.8%
References:8
References:8
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 6p22.1; Reported Gene(s): HIST1H1D; Risk Allele: rs10946808-?); (p-value= 0.000000000006).This variant is associated with Height.] [OMIM:?] [GWAS:Height] [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphisms. Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. Assessing the impact of global versus local ancestry in association studies. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. [PharmGKB:Non-Curated GWAS Results: Many sequence variants affecting diversity of adult human height (Initial Sample Size: 30,968 individuals; Replication Sample Size: 8,541 individuals).] [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
Frequency: 49.6%
References:1
References:1
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
Frequency: 50.4%
References:1
References:1
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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23andMe blog Each A of rs6854783 was associated with faster growth around the time of puberty, but was not significantly related to adult height. [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 12; STQTL12] [GWAS:Height]
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[GWAS:Height]
Frequency: 51.3%
References:1
References:1
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[GWAS:Height]
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[GWAS:Height]
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Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. Genome-wide association study identifies two novel loci containing FLNB and SBF2 genes underlying stature variation. Assessing the impact of global versus local ancestry in association studies. [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS Results: Common variants in the GDF5-UQCC region are associated with variation in human height (Initial Sample Size: 6,669 individuals; Replication Sample Size: 28,801 individuals).] [GWAS:Height]
Frequency: 53.1%
References:1
References:1
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[GWAS:Height]
0.34cm taller on average
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rs910316 is a SNP in the transmembrane emp24-like trafficking protein 10 TMED10 gene. A study of ~20,000 individuals found several SNPs associated with taller stature (height). The rs910316(T) allele was associated with an increase in height of 0.34cm per copy of the allele. [PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 14q24.3; Reported Gene(s): TMED10); (p-value= 0.0000001).This variant is associated with Height.]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS Results: Identification of ten loci associated with height highlights new biological pathways in human growth (Initial Sample Size: 15,821 individuals; Replication Sample Size: 13,671 individuals).] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 12; STQTL12] [GWAS:Height]
Frequency: 54.1%
References:2
References:2
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[PharmGKB:Non-Curated GWAS Results: Common variants in the GDF5-UQCC region are associated with variation in human height (Initial Sample Size: 6,669 individuals; Replication Sample Size: 28,801 individuals).] [GWAS:Height]
Frequency: 54.5%
References:1
References:1
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[GWAS:Height]
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[GWAS:Height]
Frequency: 55.8%
References:4
References:4
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[GWAS:Height]
Frequency: 56.2%
References:1
References:1
normal
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rs11809207 is a SNP in the cation channel, sperm associated 4 CATSPER4 gene. A study of ~20,000 individuals found several SNPs associated with taller stature (height). The rs11809207(A) allele was associated with an increase in height of 0.46cm per copy of the allele. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. [PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 1p36.11; Reported Gene(s): CATSPER4); (p-value= 0.00000006).This variant is associated with Height.]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
Frequency: 57.7%
References:2
References:2
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[GWAS:Height]
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[GWAS:Height]
Frequency: 58.4%
References:1
References:1
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[GWAS:Height]
Frequency: 59.3%
References:1
References:1
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rs10734652 is a SNP in the SET binding factor 2 SBF2 gene. Based on a study of 1000+ Caucasians and 2,000+ Chinese, rs10734652 was 'suggestively' (p=0.07) associated with height in Caucasians, as well as in Chinese subjects (p=0.048). [OMIM:?]
Frequency: 59.3%
References:1
References:1
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Testing for genetic association taking into account phenotypic information of relatives. [GWAS:Height]
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Adult height variants affect birth length and growth rate in children. [GWAS:Height]
Frequency: 60.2%
References:5
References:5
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 18q11.2; Reported Gene(s): CABLES1); (p-value= 0.000006).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. Assessing the impact of global versus local ancestry in association studies. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. [GWAS:Height]
Frequency: 64.3%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 6p21.33; Reported Gene(s): HLA-B; Risk Allele: rs13437082-?); (p-value= 0.00000005).This variant is associated with Height.] [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. [GWAS:Height]
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23andMe blog *rs1867138(T;T) or rs1867137(G;G) were approximately one inch taller than rs1867138(C;C) *rs9834312(G;G) or rs939882(G;G) increased height
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23andMe blog *rs1867138(T;T) or rs1867137(G;G) were approximately one inch taller than rs1867138(C;C) *rs9834312(G;G) or rs939882(G;G) increased height Genome-wide association study identifies two novel loci containing FLNB and SBF2 genes underlying stature variation.
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[GWAS:Height]
Frequency: 68.5%
References:1
References:1
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[GWAS:Height]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 4q31.22; Reported Gene(s): HHIP); (p-value= 0.000004).This variant is associated with Height.] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 12; STQTL12] [GWAS:Height] [GWAS:Height]
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[OMIM:?] [GWAS:Height]
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[GWAS:Height]
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[OMIM:FINGERS, RELATIVE LENGTH OF] [GWAS:Height]
Frequency: 75.2%
References:1
References:1
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[GWAS:Height]
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[GWAS:Height]
Frequency: 78.8%
References:1
References:1
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. [GWAS:Height]
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[GWAS:Height]
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[GWAS:Height]
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Ghrelin receptor gene polymorphisms and body size in children and adults. Association studies on ghrelin and ghrelin receptor gene polymorphisms with obesity. Association of maternally inherited GNAS alleles with African-American male birth weight. Family and population-based studies of variation within the ghrelin receptor locus in relation to measures of obesity. Genetic variation of the ghrelin signaling system in females with severe alcohol dependence. The ghrelin signalling system is involved in the consumption of sweets. Human longevity and variation in GH/IGF-1/insulin signaling, DNA damage signaling and repair and pro/antioxidant pathway genes: cross sectional and longitudinal studies. GH secretagogue receptor gene polymorphisms are associated with stature throughout childhood. [G...
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 4q21.21; Reported Gene(s): PRKG2); (p-value= 0.00000002).This variant is associated with Height.] [GWAS:Height]
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[GWAS:Height]
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An ambiguous flip whose risk allele could not be determined from the original data Risk alleles for multiple sclerosis identified by a genomewide study. PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm. An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. Genetic variants in the HLA-DRB1 gene are associated with Kashin-Beck disease in the Tibetan population. [GWAS:Rheumatoid arthritis]
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Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. Assessing the impact of global versus local ancestry in association studies. [GWAS:Height]
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Each copy of the G allele associates with increased height in Chinese [PharmGKB:Non-Curated GWAS results: Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. (Initial Sample Size: 618 Chinese individuals; Replication Sample Size: 2,953 Chinese individuals); (Region: 9q22.23; Reported Gene(s): ZNP510; Risk Allele: rs10816533-C); (p-value= 0.000002).This variant is associated with Height.]
normal height
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rs6060369 is a SNP associated with a (slight) increase in height, in that individuals tend to be 0.44cm taller for each rs6060369(C) allele they carry. This finding was statistically significant (p=9.7x10e-7), and ultimately tested in over 28,000 individuals. A haplotype of rs6060369 and rs143383, a neighboring SNP in the GDF5 gene, can be defined, which also links height to osteoarthritis since rs143383 has previously been linked to osteoarthritis. Medpage article Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. Assessing the impact of global versus local ancestry in association studies. [PharmGKB:Non-Curated GWAS Results: Common variants in the GDF5...
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Associated with baseline cholesterol levels in a study of 9,000+ individuals in Washington County, Maryland. [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs2016520 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0056 Type of association: PD; CO]
common in complete genomics
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Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. [GWAS:Height]
Magnitude: 0
Frequency: 82.1%
Repute:Good
References:1
Frequency: 82.1%
Repute:Good
References:1
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[GWAS:Height]
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:2
Frequency: 85.0%
Repute:Good
References:2
common on affy axiom data
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Genome-wide association scan identifies a prostaglandin-endoperoxide synthase 2 variant involved in risk of knee osteoarthritis. A genome-wide association study of northwestern Europeans involves the C-type natriuretic peptide signaling pathway in the etiology of human height variation. Assessing the impact of global versus local ancestry in association studies. [GWAS:Height]
Magnitude: 0
Frequency: 88.4%
Repute:Good
References:1
Frequency: 88.4%
Repute:Good
References:1
Magnitude: 0
Frequency: 93.8%
Repute:Good
References:1
Frequency: 93.8%
Repute:Good
References:1
Magnitude: 0
Frequency: 93.8%
Repute:Good
References:1
Frequency: 93.8%
Repute:Good
References:1
Magnitude: 0
Frequency: 94.7%
Repute:Good
References:1
Frequency: 94.7%
Repute:Good
References:1
common in complete genomics
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height being the quantitative trait associated with in [GWAS:Quantitative traits]
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[GWAS:Height]
192 snps
(hide) Hemochromatosis
complex! see rs4880
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The rs4880(T) allele, part of the codon for amino acid valine at codon 16 of the antioxidant protein from the mitochrondrial superoxide dismutase 2 SOD2 gene, is the most common in most populations studied. The rs4880(C) allele gives rise to an alanine at this position is it also known as Val16Ala manganese superoxide dismutase, or A16V. There appears to be some conflict in the literature over the effect of this SNP. Having a valine at codon 16 is said to reduce enzyme activity , and thus lead to increased oxidative stress, yet in at least one study of the actual enzyme levels measured in people, SOD2 activity was 33% higher in (C;T) or (T;T) individuals compared to (C;C) individuals . Regardless of how this resolves, several phenotypic associations have been reported for this SNP, includi...
higher transferrin levels if rs1800562(A;A)
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rs235756, a relatively common SNP in the BMP2 gene, has been associated with higher serum transferrin levels - and presumably therefore higher risk for developing hemochromatosis - in the rare individuals who are rs1800562(A;A) homozygotes, i.e. those known as C282Y homozygotes. [OMIM:BONE MORPHOGENETIC PROTEIN 2; BMP2]
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y or Cys282Tyr mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who act...
normal
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hemochromatosis related; better known in dbSNP nomenclature as rs1800730 https://en.wikipedia.org/wiki/HFE_hereditary_haemochromatosis discussion at 23andMe
Not a H63D hemochromatosis carrier.
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rs1799945, also known as H63D or His63Asp, represents a SNP that accounts for a mild form of hereditary hemochromatosis (HH), an iron overload condition in which mutations of certain genes involved in iron metabolism disrupt the body’s ability to regulate uptake of iron, causing increased intestinal iron absorption. The most common form is caused by mutations in the HFE gene, which are inherited recessively. The gene for HH is closely linked to the HLA-A3 locus on the short arm of chromosome 6 . In 1996, HFE, a gene for HH, was found to have two missense mutations . A mutation at amino acid 282 (C282Y) was found to be homozygous in 83 percent of patients with HH. This is a point mutation from guanine to adenine, resulting in a missense mutation from cysteine to tyrosine. Such mutatio...
common in clinvar
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rs1800730, also known as S65C or Ser65Cys, is associated with a mild form of hemochromatosis ; in SNPedia, see also i3002468. [OMIM:?]
6 snps
(hide) Hemophilia
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
13 snps
(hide) Hepatitis C
Frequency: 54.9%
References:24
References:24
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23andMe blog rs8099917(C) less likely to respond to Hepatitis C treatment. rs12979860(C;C) better able to become naturally Hepatitis C virus-free. rs12980275(A) usually corresponds to the rs12979860(C) Variants in IL28B in liver recipients and donors correlate with response to peg-interferon and ribavirin therapy for recurrent hepatitis C. Importance of IL28B gene polymorphisms in hepatitis C virus genotype 2 and 3 infected patients. Predictive value of the IL28B polymorphism on the effect of interferon therapy in chronic hepatitis C patients with genotypes 2a and 2b. Peginterferon and ribavirin treatment for hepatitis C virus infection. IL28B polymorphisms predict reduction of HCV RNA from the first day of therapy in chronic hepatitis C. IL28B polymorphisms, IP-10 and viral load predict v...
common
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23andMe blog rs8099917(C) less likely to respond to Hepatitis C treatment. rs12979860(C;C) better able to become naturally Hepatitis C virus-free. rs12980275(A) usually corresponds to the rs12979860(C) [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: This variant is associated with null virological response (NVR) and sustained virologic response (SVR) in Janapese patients with hepatitis C virus infection treated with PEG-INF-alpha plus ribavirin. Study size: Initial sample:154; Replication Sample: 172. Study population/ethnicity: Japanese. Significance metric(s): P=3.11 x 10(-15) (NVR); P = 1.11 x 10(-27)(SVR). Type of association: GN; CO] [OMIM:INTERLEUKIN 28B; IL28B] [GWAS:Response to Hepatitis C treatment]
common in complete genomics
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rs3792323 associates with the outcome of IFN therapy in patients with chronic hepatitis C genotype 1b
3 snps
(hide) Hereditary fructosuria
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Hereditary fructose intolerance rs387906225
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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'''WARNING!''' The orientation of this SNP was flipped from being on the FWD strand in the human genome assembly GRCh37 to being on the REV strand in assembly GRCh38 and is therefore currently prone to confusion. rs1800546 is located on chromosome 9q31.1 within the aldolase B fructose bisphosphate ALDOB gene. rs1800546 is linked to approximately 65% of hereditary fructose intolerance (HFI) cases in those of European ancestry. The incidence of HFI in those of European ancestry is estimated to be 1 in 20,000 births. HFI is an autosomal recessive condition. Since this is a minus strand SNP as of GRCh38, it is an ambiguous flip prone to some confusion, but to be clear, in SNPedia the orientation for the ancestral allele of this SNP is now C, while the risk-associated allele is G. [Note: Report...
5 snps
(hide) Hereditary hemorrhagic telangiectasia type 2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
2 snps
(hide) Herpes
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associations with schizophrenia and herpes rs2272127 with schizophrenia(P = 0.0007, odds ratio for C allele 1.49, 95% CI: 1.18-1.87; P = 0.03 following correction for multiple comparisons). rs2272127 was also associated with herpes simplex virus 1 (HSV1) seropositivity in cases (P = 0.04, OR for G allele 1.58, 95% CI: 1.04-2.39).
1 snp
(hide) High blood pressure
A1/A2: Bad at avoidance of errors. 0.5x lower OCD risk, 0.87x lower Tardive Diskinesia risk, higher ADHD risk. More Alcohol Dependence. Lower risk of Postoperative Nausea. Increased obesity. Bupropion is not effective. The DRD2 TaqIA A1/A2 version causes less dopamine receptors. Doesn't learn from mistakes well. Reduced response to errors and increased addictive behavior Men may have half the risk of Obsessive Compulsive Disorder but higher risk of ADHD. Women have lower Persistence. 0.87x reduced risk of Tardive Diskinesia when taking dopamine receptor antagonists. Slightly increased risk of alcoholism and smoking addiction. Slower recovery from traumatic brain injury. Lower risk of postoperative nausea within 6 hours of surgery. Bupropion (Wellbutrin, Budeprion, Prexaton, Elontril, Aple...
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain . Reduced response to errors and increased addictive behavior It has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessa...
some risk linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil).
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
~1.4x increased risk of hypertension
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rs5186, a SNP known as +1166A/C or A1166C, is located in the 3' untranslated region of the angiotensin II receptor type 1 gene AGTR1, which is also known as AT2R1 or AT1R. It is among the most studied of over 50 SNPs in AGTR1. The rs5186(C) allele is associated with increased risk for essential hypertension in Caucasian populations with an odds ratio of 7.3 (homozygote (C;C) compared to (A;C) and (A;A), CI: 1.9-31.9,p=0.0015). There are likely to be ethnic differences in risk; while the rs5186(C) allele was associated with hypertension in a Chinese population , it was not been observed as a risk in a Japanese population. Age and gender may also influence risk, as discussed in a review of AGTR1 SNPs and their role in hypertension and related disorders. Pregnant women who are rs5186(C) allel...
increased risk of hypertension
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rs699 is a SNP in the angiotensin AGT gene that encodes a functional change. In most published literature, the name for this SNP is M235T, or perhaps Met235Thr, however its amino acid 268 (not 235) that varies based on the numbering in todays databases. rs699 is also occasionally known as C4072T. In any case, the rs699(C) allele encodes the threonine variant, which is associated with higher plasma angiotensin levels, and ultimately higher blood pressure leading to increased risk for hypertension associated disorders. This association was first reported in 1992 , and many studies, though not all, have replicated these findings. rs699 is also (generally) reported to be in tight linkage with rs5051, a neighboring SNP in the promoter of the AGT gene. rs699(C) has also been implicated as a risk...
1.8x increased risk for high blood pressure
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rs4961 is a variation in the adducin 1 ADD1 gene, encoding a change from a glycine to a tryptophan, so it is also known as G460W or Gly460Trp. Originally, a study of 477 Italian patients indicated that carriers of one or two rs4961(T) alleles were at 1.8x increased risk for hypertension (CI: 1.32-2.43). This study also indicated that carriers of the risk (T) allele responded better to diuretics and sodium-restricted diets, in that they tended to lower their blood pressure by ~10 mmHg points compared to rs4961(G;G) homozygotes similarly treated. Subsequent studies have tended to confirm this association, and to extend it to risk for heart disease. They also have tended to confirm that risk allele carriers respond better to therapy. In a study of ~2200 Belgian patients, rs4961(T) carriers we...
1.2x higher risk for hypertension
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rs6997709 has been reported in a large study to be associated with high blood pressure. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.20 (CI 0.94-1.52), and for homozygotes, 1.49 (CI 1.18-1.89). In a study of 7,551 Koreans, this SNP was associated with systolic and diastolic blood pressures in a quantitative trait association test but no associations were found using a case-control association test.
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
Slightly increased risk for pregnancy-induced hypertension
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rs2881766 is a SNP in the promoter region of the estrogen receptor alpha ESR1 gene. Carriers of rs2881766(T) alleles are at somewhat (slightly) higher risk for pregnancy-induced hypertension.
responds well to bucindolol; may also depend on rs1801252
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
1.3x high blood pressure risk
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rs11110912 has been reported in a large study to be associated with high blood pressure. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.33 (CI 1.18-1.51), and for homozygotes, 1.34 (CI 0.96-1.86).
Frequency: 8.0%
References:1
References:1
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[GWAS:Hypertension]
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rs4149601 has been associated with hypertension. This SNP by itself was associated with diastolic blood pressure (DBP) (p=0.03) and DBP progression over time (p=0.04); in genotypic combination with intronic NEDD4L SNP rs2288774 it was associated with systolic blood pressure (SBP) (p=0.01), DBP (p=0.04), and progression of both SBP (p=0.03) and DBP (p=0.05) over time. Polymorphism in NEDD4L is associated with increased salt sensitivity, reduced levels of P-renin and increased levels of Nt-proANP. Expression, transcription, and possible antagonistic interaction of the human Nedd4L gene variant: implications for essential hypertension. Two polymorphisms in NEDD4L gene and essential hypertension in Chinese Hans - a population-based case-control study. Physiological interaction between alpha-ad...
increased risk for hypertension
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rs5051 is a SNP in the promoter of the angiotensin AGT gene, and presumably due to it's tight linkage with rs699, the rs5051(T) allele - as oriented to the dbSNP entry, not as published - has been associated with increased risk for hypertension and complications thereof. rs699(T) is associated with higher plasma angiotensinogen levels, and therefore the increased risk of essential hypertension. The frequency of the rs699(T) allele is also generally higher in African populations compared to Caucasian populations, correlating to the higher incidence of hypertension in African population. rs5051 is also known as 'A-6G'. For more details, see rs699. rs5051(T;T) homozygotes have been reported to be at increased risk for Crohn's disease, as based on one cohort of ~350 Australian patients. The od...
1.5x risk
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rs2820037 has been reported in a large study to be associated with high blood pressure. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.54 (CI 1.03-2.31), and for homozygotes, 1.09 (CI 0.74-1.62). Replication of the Wellcome Trust genome-wide association study of essential hypertension: the Family Blood Pressure Program. Using a latent growth curve model for an integrative assessment of the effects of genetic and environmental factors on multiple phenotypes. [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,952 cases, 2,938 controls; Replication Sample Size: NR; Risk Allele: rs2820037-T). This variant is associated with hyperten...
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In 'Association of the ADRA2A polymorphisms with the risk of type 2 diabetes: a meta-analysis.' a meta-analysis of publications prior to September 2012 showed no overall association between rs553668 and T2D risk, but did find an association with very high (poor) P-value for Europeans under recessive gene model (GT=AA, OR=1.36, p=0.02, 95% CI: 1.05, 1.76). In 'Genetic association of adrenergic receptor alpha 2A with obesity and type 2 diabetes.' rs553668 was found to correlate with obesity in Swedish population, but not significantly for BMI-corrected T2D risk. ADRA2A is involved in sympathetic nervous system's inhibition of insulin secretion and lipolysis, so direct effect on T2D is usually sought, but the Swedish study suggest it could work through body mass. It also mentions that rs55366...
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SNP rs2827196 has been associated with both diastolic blood pressure and systolic blood pressure in the Framingham Heart Study datasets, and is thus associated with high blood pressure and heart disease. source
better response to certain calcium channel blockers
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rs3774426 is a SNP in the calcium channel, voltage-dependent, L type, alpha 1D subunit CACNA1D gene. A study of 161 Japanese patients (85 men, 76 women) being treated for hypertension with L-type dCCBs (calcium channel blockers) concluded that individuals with rs3774426(C;C) genotypes responded better, as measured by lowered systolic and diastolic blood pressure readings.
higher blood pressure if <50
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rs8192678 encodes a SNP also known as Gly482Ser; the (A) allele encodes the Ser. Some reports have linked this SNP to risk for hypertension and systolic blood pressure (SBP). However, a meta-analysis of 13,000+ individuals did not find any such association. However, gene-age interaction was apparent. For diastolic blood pressure (DBP), p(interaction)<0.0001; for systolic BP, p(interaction)=0.026. In younger individuals (<50yrs; n=2511) the rs8192678(A) allele was associated with higher DBP (p=4.2 x 10<sup>-12</sup>) and SBP (p=7.2 x 10<sup>-12</sup>), but no association was evident for individuals over 50yrs (n=5088). Analysis of PGC-1alpha variants Gly482Ser and Thr612Met concerning their PPARgamma2-coactivation function. PPARGC1A coding variation may initiat...
lower blood pressure
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A study of ~15,000 Europeans found that increased circulating natriuretic peptide and thus lower blood pressure and hypertension were associated with SNPs rs17376328(A), rs5068, rs198358(C), rs632793(G) 23andMe blog Natriuretic peptide system gene variants are associated with ventricular dysfunction after coronary artery bypass grafting. Dissecting complex traits: recent advances in hypertension genomics. Novel associations of CPS1, MUT, NOX4, and DPEP1 with plasma homocysteine in a healthy population: a genome-wide evaluation of 13 974 participants in the Women's Genome Health Study. Association of common variants in NPPA and NPPB with blood pressure does not translate into kidney damage in a general population study. Association of genetic variation in the natriuretic peptide system with...
1.3x risk
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rs1937506 has been reported in a large study to be associated with high blood pressure. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.33 (CI 1.04-1.69), and for homozygotes, 1.60 (CI 1.26-2.02). As follows from results of Replication of the Wellcome Trust genome-wide association study of essential hypertension this SNP (rs1937506) only one of the top 6 SNPs which might be associated with essential hypertension in Americans of European origin. This SNP shows a significant but opposite effect in Americans of Hispanic origin. Each additional G allele of rs1937506 is associated with a 24.9 mmHg decrease of systolic blood pressure (SBP) in European Americans and with a 27.7 mmHg increase in Hispanic Americans. Considering diastolic blood...
2x increased hypertension risk
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rs3781719 is a SNP, also known as T-692C, in the calcitonin-related polypeptide alpha CALCA gene. A study of 293 Chinese subjects with essential hypertension (EH) and 208 controls concluded that rs3781719(C) allele carriers were associated with increased EH risk (odds ratio 2.093, CI: 1.317-3.326, p<0.01).
1.3x risk for hypertension
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rs3755351, a SNP in the ADD2 gene, was associated with risk for hypertension in a study involving 1,500+ Japanese patients. The odds ratio associated with the risk allele, rs3755351(C), which is also the most common allele, is 1.30 (CI: 1.15 - 1.46, p = 0.00002). Note that a neighboring ADD2 SNP in close (r2 of 0.806) proximity, rs17006246, was associated with hypertension in a diabetes study ; however, in this case, it was in 'the opposite direction of effect'. This discrepancy has not been resolved.
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rs700518 is a SNP potentially linked in a gender-specific manner to hypertension [OMIM:CYTOCHROME P450, FAMILY 19, SUBFAMILY A, POLYPEPTIDE 1; CYP19A1]
normal
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rs6749447 is a SNP in the serine threonine kinase 39 STK39 gene. A study of ~1,000 Amish originally identified rs6749447 and another SNP also in the STK39 gene, rs3754777, as being significantly associated with hypertension. This association was then found to also hold in patient data analyzed from the Framingham Heart Study and the Diabetes Genetics Initiative. On average, each minor allele, in this case rs6749447(G), is associated with 2.0 mmHg higher systolic blood pressure and a 1.0 mm Hg higher diastolic pressure. [PharmGKB:Non-Curated GWAS results: Whole-genome association study identifies STK39 as a hypertension susceptibility gene. (Initial Sample Size: 542 individuals; Replication Sample Size: 6,583 individuals); (Region: 2q24.3; Reported Gene(s): STK39; Risk Allele: rs6749447-G)...
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rs10046 is a SNP potentially linked in a gender-specific manner to hypertension rs10046(C;C) associated with miscarriages (P = 0.017) Polymorphisms associated with circulating sex hormone levels in postmenopausal women. Multilocus analysis of SNP and metabolic data within a given pathway. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Sex and body mass index specific regulation of blood pressure by CYP19A1 gene variants. Genome-wide association with bone mass and geometry in the Framingham Heart Study. Single nucleotide polymorphisms of the aromatase gene (CYP19A1), HER2/neu status, and prognosis in breast cancer patients. Association between single-nucleotide polymorphisms in hormone metabolism and DNA repai...
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rs2266917, located in the ATP6B1 gene, passed adjustments for multiple testing and had a significant independent main effect (p = 0.0018) on diastolic high blood pressure among African-American women, based on a study of 1418 African-American women and men from the Genetic Epidemiology Network of Arteriopathy study.
Frequency: 49.2%
References:4
References:4
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A variant upstream of the CDH13 adiponectin receptor gene and metabolic syndrome in Swedes. Dissecting complex traits: recent advances in hypertension genomics. [PharmGKB:Non-Curated GWAS results: Genome-wide scan identifies CDH13 as a novel susceptibility locus contributing to blood pressure determination in two European populations. (Initial Sample Size: 364 cases, 590 controls; Replication Sample Size: 1,043 cases, 1,769 controls); (Region: 16q23.3; Reported Gene(s): CDH13; Risk Allele: rs11646213-T); (p-value= 0.000008).This variant is associated with Hypertension.] [GWAS:Hypertension]
Magnitude: 1
Frequency: 67.3%
Repute:Bad
References:2
Frequency: 67.3%
Repute:Bad
References:2
common but slightly higher risk for hypertension
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rs13333226 is a SNP in the 5' region of uromodulin UMOD gene. A large GWAS study ultimately totaling over 20,000 cases and almost as many controls concluded that, compared to the far more common allele, the rarer rs13333226(G) allele is associated with a (slightly) lower risk of hypertension (odds ratio 0.87, CI: 0.84-0.91) as well as a 7.7% reduction per allele for risk of cardiovascular events after adjusting for age, sex, BMI, and smoking status (hazard ratio?0.923, CI: 0.860-0.991; p?=?0.027). High Blood Pressure (Hypertension) Kidney Disease
Frequency: 87.6%
References:1
References:1
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[GWAS:Hypertension]
>1.19x risk for hypertension
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rs5335, a SNP in the EDNRA gene, has been associated with a (slightly) increased risk for hypertension, based on a study of ~1400 Caucasians. The odds ratio per (G) allele is 1.19 (CI: 1.00-1.41, p=0.05). A role for endothelin receptor type A in migraine without aura susceptibility? A study in Portuguese patients.
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rs4963 is in very tight linkage with rs4961, another ADD1 gene SNP, and thus linked to hypertension. The rs4963(C) allele is the more common, predicting (the more common) rs4961(G) allele; the rs4963(G) allele is less common, predicting the rs4961(T) - and risk - allele. See rs4961 for details.
average
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rs1805762, a SNP in the M6PR gene, was associated with risk for hypertension in a study involving 1,500+ Japanese patients. The odds ratio associated with the risk allele, in dbSNP orientation, rs1805762(G), which is also the most common allele, is 1.23 (CI: 1.10 - 1.37, p = 0.0003). A SNP in close linkage, rs1805740, has also been reported in association with hypertension risk in the large 2007 study reported by the Wellcome Trust Consortium.
normal
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rs2398162 has been reported in a large study to be associated with high blood pressure. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 0.97 (CI 0.76-1.25), and for homozygotes, 1.31 (CI 1.03-1.67). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,952 cases, 2,938 controls; Replication Sample Size: NR; Risk Allele: rs2398162-A). This variant is associated with hypertension.] [GWAS:Hypertension]
normal
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rs7961152 has been reported in a large study to be associated with high blood pressure. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.16 (CI 1.01-1.32), and for homozygotes, 1.47 (CI 1.25-1.74). This SNP was just about the only one tested to replicate as associated with hypertension in a study of 7,551 Koreans patients, with an odds ratio of 1.28 (CI: 1.012-1.636, p=0.04) but only in one of two cohorts.
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
better response to certain calcium channel blockers
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rs312481 is a SNP in the calcium channel, voltage-dependent, L type, alpha 1D subunit CACNA1D gene. A study of 161 Japanese patients (85 men, 76 women) being treated for hypertension with L-type dCCBs (calcium channel blockers) concluded that individuals with rs312481(C;C) genotypes responded better, as measured by lowered systolic and diastolic blood pressure readings.
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23andMe blog each G at rs4293393 decreased the odds of chronic kidney disease by 24%. Approximately 18% of people with European ancestry have at least one G at this SNP. DeCode reports that the T allele of rs4293393 is associated with kidney stones and chronic kidney disease. This SNP may also be associated with susceptibility to gout], hypertension, and diabetes.
normal
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rs3754777 is a SNP in the serine threonine kinase 39 STK39 gene. A study of ~1,000 Amish originally identified rs3754777 and another SNP also in the STK39 gene, rs6749447, as being significantly associated with hypertension. This association was then found to also hold in patient data analyzed from the Framingham Heart Study and the Diabetes Genetics Initiative. On average, each minor allele, in this case rs3754777(A), is associated with 2.0 mmHg higher systolic blood pressure and a 1.0 mm Hg higher diastolic pressure. High Blood Pressure (Hypertension)
normal
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SNP rs4399848 (Chr 3 at 28.679467 Mb, band 3p24.1, dbSNP build 128) is associated weakly with hypertension in a genome-wide association study by the Wellcome Trust Case Control Consortium published in Nature (2007, appendix Table 7, page 40) . The so-called single point P is less than 0.0004 (4.44E-04). This statistic is relatively uninformative without follow-up study and a larger sample size. The (G;G) genotype is ancestral and has a frequency close to 100% in the Yourba population (Ibadan, Nigeria) and approximately 96-98% in Han Chinese. The (A;G) heterozygote has a frequency of up to about 25% in some European populations (Perlegen and HapMap). The (A;A) minor genotype is rare. The presumed effects of the A allele on risk of hypertension are likely to be very low and are still controv...
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:0
Frequency: 85.8%
Repute:Good
References:0
normal
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A study of ~15,000 Europeans found that increased circulating natriuretic peptide and thus lower blood pressure and hypertension were associated with SNPs rs17376328(A), rs5068, rs198358(C), rs632793(G) 23andMe blog
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A study of ~15,000 Europeans found that increased circulating natriuretic peptide and thus lower blood pressure and hypertension were associated with SNPs rs17376328(A), rs5068, rs198358(C), rs632793(G) 23andMe blog
common in complete genomics
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Repeatedly associated with increased body mass index and hypertension according to
normal
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rs3731566 is a SNP in the adducin 3 ADD3 gene. This variation on its own has not been linked to hypertension. However, carriers of a rs4961(T) SNP (a SNP in the ADD1 gene) who also happen to be rs3731566(G;G) homozgyotes are found to have higher blood pressure (by about 8 mmHg) than if they are carriers of one or more rs3731566(A) alleles.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
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rs61753344 is a SNP in the FMO3 gene. It has been reported in both homozygous and heterozygous forms to potentially be linked to trimethylaminuria; in the homozygous form, it has also been linked to tachycardia and severe hypertension after eating cheese (which contains tyramine) and after using nasal epinephrine. [OMIM:?]
46 snps
(hide) Hirschsprung disease
normal
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Associated with protection from Hirschsprung disease See OMIM 164761.0052 [OMIM:?]
Magnitude: 0
Frequency: 98.4%
Repute:Good
References:2
Frequency: 98.4%
Repute:Good
References:2
normal
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A complex pattern of mutations involving rs17158558(T) and other mutations simultaneously occurring may - or with greater odds, actually, may not - lead to Hirschsprung disease. [OMIM:HIRSCHSPRUNG DISEASE]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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This SNP, located in the first intron of the RET gene, has been associated with Hirschsprung disease. The risk allele (in dbSNP orientation) is rs2435357(A), with greater affect in males. [OMIM:REARRANGED DURING TRANSFECTION PROTOONCOGENE; RET]
9 snps
(hide) HIV
60% reduction in HIV viral load The rs9264942(C;T) genotype is reported to be associated with a 60% reduction in viral load in HIV-infected individuals. See also rs9264942 and HIV.
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This SNP (C/T) is in 5' region of the HLA-C gene, 35 kb away from transcription initiation in or around the HLA-C gene. 'People with this tiny sequence variation, dubbed rs9264942, appear to have up to 90% less virus in their systems than those who carry other polymorphisms. About 10% of Europeans appear to carry two copies of rs9264942, which leads to an average 90% viral load reduction. About 50% of Europeans carry one copy, which gives a 60% reduction. By comparison, less than 40% of people of African descent appear to carry a single copy of the polymorphism.' Genetic variation may lower HIV load by 90% They are referring to the (C;C) genotype giving a 90% reduction and the (C;T) giving a 60% reduction. dbSNP page This SNP is also reported to account for 6.5% of the 15% variation in vir...
complex; generally greater risk for cancer progression
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rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and H131R. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...
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Rs2856758 is a SNP in the CCR5 gene (CC-chemokine receptor type 5). Variants in CCR5 are associated with resistance to HIV infection. Another mutation in this gene, rs333] (also known as the CCR5-delta32 deletion), is associated with resistance to HIV. This mutation may have spread in the European population in response to selection pressure from plague (Black Death) or smallpox. [http://www.pnas.org/content/100/25/15276.long] Polymorphisms in the CC-chemokine receptor-2 (CCR2) and -5 (CCR5) genes and risk of coronary heart disease among US women. Genetic variation within the gene encoding the HIV-1 CCR5 coreceptor in two South African populations. Host and viral genetic correlates of clinical definitions of HIV-1 disease progression.
normal risk
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rs1024611, also known as the -2578A>G SNP due to its position in the promoter of the monocyte chemoattractant protein-1 MCP-1 CCL2 gene, influences the production of its corresponding protein, a chemokine involved in inflammatory responses. In a study focusing on 679 apparently healthy siblings of people with premature heart disease, investigators found that carriers of an rs1024611(C) allele - oriented as in dbSNP, not as published - independently predicted the risk of exercise induced ischemia in general. The odds ratio was reported to be 1.86 (CI: 1.14-3.04, p=0.014), regardless of race, age, sex and other factors. However, it is not clear if this risk carries over to individuals who lack siblings with heart disease. discussed in the 23andMe blog as being relevant to HIV rs1024611 is...
common, but faster HIV progression
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23andMe blog females with one copy of rs5968255(C) progressed from HIV infection to AIDS more slowly with an average of eight years, nearly four times more than females with no copies or males. The search for host genetic factors of HIV/AIDS pathogenesis in the post-genome era: progress to date and new avenues for discovery. Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations? HIV Progression
normal
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rs2572886 is a SNP determined by both linkage studies and in-vitro experiments to increase the susceptibility to infection by HIV. The risk allele, rs2572886(A), yields an odds ratio of 1.4 (p=0.001), and also appears to be associated with higher viral load and faster disease progression. blog
common The rs2395029(T;T) genotype is the common genotype for this SNP, against which the rs2395029(T;G) and rs2395029(G;G) genotypes that are associated with reduced HIV viral load in HIV carriers are compared. See also rs9264942 and HIV.
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rs2395029 is a SNP in the major histocompatibility complex (MHC) region, and several studies have shown that the rs2395029(G) allele is 99.9% predictive of the presence of an HLA-B*5701 allele. This HLA allele, in turn, has been associated with several conditions. A study of 51 cases of flucloxacillin drug-induced liver injury (DILI), an important cause of serious liver disease, along with a replication study of another 23 cases, found that the rs2395029(G) carriers were at highly increased risk (odds ratio 80, p=8.7x10(-33)). * see also: 23andMe blog rs2395029(G;G) increases the odds of drug-induced liver injury in response to flucloxacillin by 45x This SNP is thought to be involved in determining the HIV viral load set point during the asymptomatic period of infection. This SNP is estima...
not resistant to HIV
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this snp is on the 23andMe microarray but lacks a dbSNP identifier. discussed in the 23andMe blog *II +/+: Not resistant to HIV infection; shows average time of progression to AIDS after infection. *DI Delta32/+: Not resistant to HIV infection but may have slower progression to AIDS after infection. *DD Delta32/Delta32: Resistant to infection by the most common strain of HIV people usually encounter, though protection is not complete. Article also seems to discuss rs333 (aka CCR5Delta32) Resistance to HIV/AIDS
8 snps
(hide) Hodgkin lymphoma
3.5x increased risk for Hodgkin lymphoma
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rs1585215 is a SNP in the NFKB1 gene. A population-based case-control study including 473 cases of Hodgkin lymphoma concluded that increased risk for the disease was significantly associated with rs1585215. The odds ratio for rs1585215(G;G) homozygotes was 3.5 (CI: 2.2-5.7, Ptrend = 1.7 x 10(-8)), and for (A;G) heterozygotes, 2.1 (CI: 1.5-2.9).
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[GWAS:Hodgkin's lymphoma]
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Hodgkin lymphoma [GWAS:Hodgkin's lymphoma]
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Hodgkin lymphoma [GWAS:None]
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[OMIM:?] [GWAS:Vitiligo]
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The A allele appears to protect against Hodgkin lymphoma.
7 snps
(hide) Homocystinuria
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rs1801131 is a SNP in the MTHFR gene, representing an A>C mutation at mRNA position 1298, resulting in a glu429-to-ala (E429A) substitution (hence this SNP is also known as A1298C or E429A). A diplotype (according to the authors, but perhaps actually a genoset) of rs1801131 and rs1801133 has been linked to increased risk for several types of brain cancer. The highest risk of meningioma was associated with heterozygosity for both MTHFR SNPs (odds ratio 2.11, CI: 1.42-3.12, p=0.002). The corresponding odds ratio for glioma was 1.23 (CI: 0.91-1.66, p=0.02. In general, risks were increased with genotypes associated with reduced MTHFR activity. rs1801131 shows no consistent association with schizophrenia overall in 12 studies totaling 3,000+ patients [PharmGKB:Curated Risk or phenotype-asso...
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
common in clinvar
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Regarding Homocystinuria, the I278T mutation has been associated with B6 responsiveness and a relatively mild clinical phenotype when homozygous. Lack of association of polymorphisms in homocysteine metabolism genes with pseudoexfoliation syndrome and glaucoma. Association of 77 polymorphisms in 52 candidate genes with blood pressure progression and incident hypertension: the Women's Genome Health Study. 118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects. A candidate gene association study of 77 polymorphisms in migraine. [PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The T variant of rs5742905 was associated with Spina Bifida in a transmission disequilibrium test. Study size: 610 families (329 trios, 281 duos) Study population/et...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
5 snps
(hide) Hypercholesterolemia
?
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rs7566605 was initially reported as being associated in at least 4 independent populations as being associated with obesity however replications are inconsistent, and a recent (2009) large meta-analysis comprising 34 studies (and over 70,000 subjects) has concluded that there is no evidence for overall association of the rs7566605 polymorphism with obesity. See also: Poster At least one population has since been reported in which this association was not seen. Furthermore, a study of 18,000 Danish subjects also failed to find any direct role for this SNP in the development of obesity, except that among physically inactive subjects, (C)-allele carriers tended to have a higher body mass index (by O.5 kg/m2) than (G)-allele carriers. On the other hand, a report has also been published indicat...
common in complete genomics
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rs505151 is a SNP, also known as E670G or 23968A>G, in the proprotein convertase subtilisin/kexin type 9 PCSK9 gene. rs505151(G) encodes the Gly (G), and rs505151(A) encodes the Glutamic acid (E). In a study of 506 European polygenic hypercholesterolemia patients, the rs505151(G) allele was found with increased frequency in men but not in women. rs505151 rs562556 show evidence of 'gain-of-function' mutations that are associated with higher LDL cholesterol levels. Longitudinal association of PCSK9 sequence variations with low-density lipoprotein cholesterol levels: the Coronary Artery Risk Development in Young Adults Study. The proprotein convertase subtilisin/kexin type 9 gene E670G polymorphism and serum lipid levels in the Guangxi Bai Ku Yao and Han populations. Genetic variability wi...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
4 snps
(hide) Hyperphenylalaninemia
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
6 snps
(hide) Hypertriglyceridemia
Frequency: 17.7%
References:1
References:1
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[GWAS:Hypertriglyceridemia]
Frequency: 32.1%
References:5
References:5
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Polygenic determinants of severe hypertriglyceridemia. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Triglyceride level-influencing functional variants of the ANGPTL3, CILP2, and TRIB1 loci in ischemic stroke. [PharmGKB:Non-Curated GWAS Results: Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans (Initial Sample ...
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[GWAS:Hypertriglyceridemia]
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The G allele of rs4846914 is associated with higher risk of hypertriglyceridemia. ] [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 1q42.13; Reported Gene(s): GALNT2; Risk Allele: rs4846914-G); (p-value= 0.00000004).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol] [GWAS:Triglycerides]
Frequency: 52.2%
References:21
References:21
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rs17321515 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched normolipidemic controls [PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,684 individuals; Replication Sample Size: 5,312-9,707 individuals; Risk Allele: rs17321515-A). This variant is associated with triglyceride levels.] [GWAS:Triglycerides] [GWAS:Triglycerides]
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[GWAS:None]
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[GWAS:Hypertriglyceridemia]
normal
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The ancestral allele is C. The rs7412(T) allele, also known as Arg176Cys, generally indicates the presence of an Apoε2 allele; see the ApoE page for a full discussion of the ApoE alleles and their association with Alzheimer's disease. Another SNP related to ApoE is rs429358. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs7412(C) allele were more likely to gain significant weight compared to rs7412(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs4765623, were also significantly associated with weight profiles in these patients. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity ...
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[OMIM:HYPERTRIGLYCERIDEMIA, SUSCEPTIBILITY TO]
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The T allele of rs1260326 has been associated with type 2 diabetes and hypertriglyceridemia. A fine mapping approach indicates that this SNP, rs1260326, shows the strongest association signal with metabolic phenotypes in the region that also harbors the tightly linked (r(2)=0.93) SNP rs780094, which has been previously associated with triglyceride and glucose concentrations. This SNP, rs1260326, encodes a common missense glucokinase regulatory protein gene GCKR variant. gout association, based on Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. The common P446L polymorphi...
average
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rs780094, a SNP in the GCKR gene encoding the glucokinase regulatory protein, contributes to the risk of type-2 diabetes and dyslipidaemia in mulitple populations. The effect on type 2 diabetes is probably mediated through impaired beta cell function rather than through obesity. The rs780094(A) risk allele is associated with the following traits : * higher levels of fasting serum triacylglycerol * impaired fasting and OGTT-related insulin release * dyslipidemia * somewhat reduced risk of type-2 diabetes There may also be an additive effect between this SNP and a SNP known as 'GCK -30A', rs1799884, at least on fasting serum insulin levels. rs780094 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched norm...
Magnitude: 0
Frequency: 77.9%
Repute:Good
References:18
Frequency: 77.9%
Repute:Good
References:18
common on affy axiom data
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rs17145738 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched normolipidemic controls [PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,684 individuals; Replication Sample Size: 5,312-9,707 individuals; Risk Allele: rs17145738-C). This variant is associated with triglyceride levels.] [GWAS:Triglycerides] [GWAS:Triglycerides]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 7q11.23; Reported Gene(s): MLXIPL; Risk Allele: rs714052-G); (p-value= 0.000000000000003).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
normal
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rs662799 is a SNP in the APOA5 gene. The rarer rs662799(C) allele has been associated in multiple reports (cited below) to be associated with higher triglyceride levels. Independently of triglyceride levels, perhaps, a study based on 1,864 Italian patients <45 years old at the time of their first heart attack (myocardial infarction) concluded that this SNP is associated with higher risk for an early heart attack, with a per C allele odds ratio of 1.44 (CI: 1.23-1.69, p = 6.7 × 10(-5)). This SNP has also been reported to help prevent weight gain from high fat diets. 1,073 men and 1,207 women participating in the Framingham Offspring Study rs662799 -1131T>C in modulates the effect of fat intake on BMI and obesity risk in both men and women. Individuals with at least one C allele g...
normal
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SNP rs2075291 represents a glycine to cysteine substitution at amino acid 185 of the APOA5 protein; it is also known as p.185Gly>Cys or c.553G>T. In both Chinese and non-Chinese Asians, the A allele (leading to the cysteine) is associated with higher risk for hypertriglyceridemia. The odds ratio is 4.45 (CI: 2.18-9.07, p<0.001). Heterozygosity was associated with a doubling of triglyceride levels, and all (11) rs2075291(A;A) homozygotes (as oriented relative to dbSNP, not as published) had severe hypertriglyceridemia (mean triglyceride level of 2292 +/- 447 mg/dl). [OMIM:?]
common in clinvar
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rs268, also known as LPL '''Asn291Ser''' as well as '''LPL N291S''' or '''N318S''', a SNP in the lipoprotein lipase LPL gene, has been linked to increased susceptibility to hypertriglyceridemia, heart disease, Type-2 diabetes, idiopathic venous thromboembolism. A systematic review and meta-analysis of the relationship between lipoprotein lipase Asn291Ser variant and diseases. The summary standardized mean difference (SMD) of plasma triglyceride (TG) for carriers compared with noncarriers of the Asn291Ser variant was 3.23 (P < 0.00001). The summary SMD of plasma HDL-cholsterol (HDL-C) for carriers compared with noncarriers of the Asn291Ser variant was -3.42 (P < 0.0001). The summary SMD of the association of the Asn291Ser variant with plasma TG increased with increasing age and weight...
common in clinvar
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[PharmGKB:Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of triglycerides. Study size:6382. Study population/ethnicity: Caucasian women. Significance metric(s): P = 4.7 x 10(-11). Type of association: CO; GN] [OMIM:LIPOPROTEIN LIPASE; LPL] [GWAS:HDL cholesterol]
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The rs964184(G;G) genotype is associated with hypertriglyceridemia. [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 11q23.3; Reported Gene(s): APOA1, APOC3, APOA4, APOA5; Risk Allele: rs964184-G); (p-value= 0.000000000001).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
common on affy axiom data appears to be common on the 23andMe platform
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Rs3135506 (also known as S19W) is associated with severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched normolipidemic controls. It is discussed in ; however, the SNP that prevents weight gain from high fat diets is rs662799. [PharmGKB:Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of triglycerides and apolipoprotein B. Study size:6382. Study population/ethnicity: Caucasian women. Significance metric(s): triglycerides: p = 5.5 x 10(-12); ApoB: p = 8.4 x 10(-8). Type of association: CO; GN] [OMIM:?]
20 snps
(hide) Hypokalemic periodic paralysis
common in clinvar
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rs28930069, also known as R1239G or Arg1239Gly, is a SNP in the CACNA1S gene on chromosome 1. The rs28930069(G) allele has been reported in a family study to be the basis for their hypokalemic periodic paralysis, type 1. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. [OMIM:HYPOKALEMIC PERIODIC PARALYSIS]
1 snp
(hide) Hypothyroidism
increased risk for celiac disease increased resistance to bacterial infections
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rs3184504 is a nonsynonymous SNP in the SH2B3 gene, and it is also known as R262W. In a recent (2008) study of non-HLA SNP associations of 1600+ celiac disease patients, this SNP was considered one of the most significant. The odds ratio for the minor allele was 1.19 (CI:1.10-1.30, p=1.33x10e-7). rs653178, another SNP in strong linkage disequilibrium (r<sup>2</sup>>0.99) with rs3184504, was also associated with celiac disease. associated with type-1 diabetes 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 23andMe blog blood pressure Pharmacogenetic implications for eight common blood pressure-associated...
Typical odds of developing primary hypothyroidism.
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rs7850258 is located on chromosome 9 and is 67 kb from the nearest gene, ''FOXE1''. ''FOXE1'', also known as thyroid transcription factor 2, is an intronless gene with a crucial role in thyroid morphogenesis. This SNP is associated with primary hypothyroidism. Primary hypothyroidism is the most common thyroid disorder, affecting 1-5% of the population, and is characterized by deficiencies of thyroid hormones T3 (triiodothyronine) and T4 (thyroxine). Using electronic medical record-linked DNA biobanks, a study with 1,317 cases and 5,053 controls of European American ancestry identified rs7850258 to have the strongest association with hypothyroidism. The odds ratio for the minor allele A was 0.74 (p-value = 3.96 x 10-9). This SNP was in strong pair-wise linkage disequilibrium (r2 > 0.98) ...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Analysis of body height in 829 patients with different forms of testicular pathology. Atrial form and function: lessons from human molecular genetics. Progressive AV-block and anomalous venous return among cardiac anomalies associated with two novel missense mutations in the CSX/NKX2-5 gene. Two novel frameshift mutations in NKX2.5 result in novel features including visceral inversus and sinus venosus type ASD. Phenotypes with GATA4 or NKX2.5 mutations in familial atrial septal defect. NKX2.5 mutations in patients with non-syndromic congenital heart disease. [OMIM:TETRALOGY OF FALLOT]
Not a H63D hemochromatosis carrier.
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rs1799945, also known as H63D or His63Asp, represents a SNP that accounts for a mild form of hereditary hemochromatosis (HH), an iron overload condition in which mutations of certain genes involved in iron metabolism disrupt the body’s ability to regulate uptake of iron, causing increased intestinal iron absorption. The most common form is caused by mutations in the HFE gene, which are inherited recessively. The gene for HH is closely linked to the HLA-A3 locus on the short arm of chromosome 6 . In 1996, HFE, a gene for HH, was found to have two missense mutations . A mutation at amino acid 282 (C282Y) was found to be homozygous in 83 percent of patients with HH. This is a point mutation from guanine to adenine, resulting in a missense mutation from cysteine to tyrosine. Such mutatio...
5 snps
(hide) In vitro fertilization
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rs2234693 is a SNP upstream of the estrogen alpha receptor ESR1 gene, and is sometimes referred to as the -397T>C variation. rs2234693 rs9340799 and rs1256049 variations in ESR1 gene, in addition to the age of a woman, may predict the COH outcome in in vitro fertilization A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs2234693) and risk of ischemic stroke rs2234693(C;C)more frequent in African American schizophrenics (p=0.01 to 0.001). haplotype less common in schizophrenia rs2273206(T), rs2273207(G), rs2228480(G). Oestrogen receptor alpha gene haplotype and postmenopausal breast cancer risk: a case control study. Differential genetic effects of ESR1 gene polymorphisms on osteoporosis outcomes. Estrogen receptor alpha gene varia...
common in complete genomics
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rs1256049 is a SNP in the estrogen receptor 2 gene ESR2. rs1256049(A) allele carriers have higher mean carotid artery intima-media thickness (CIMT) as well as maximal CIMT, but this result may be limited to the population studied, in this case individuals from the Cardiovascular Risk in Young Finns study. [Association between single-nucleotide polymorphisms in estrogen receptor beta gene and risk of prostate cancer]. Polymorphisms in the estrogen receptor beta (ESR2) gene are associated with bone mineral density in Caucasian men and women. Allelic estrogen receptor 1 (ESR1) gene variants predict the outcome of ovarian stimulation in in vitro fertilization. CA repeat and RsaI polymorphisms in ERbeta gene are not associated with infertility in Indian men. Haplotypes of the estrogen receptor ...
3 snps
(hide) Inflammatory bowel disease
1.2x risk Rheumatoid Arthritis
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rs6920220 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.20 (CI 1.06-1.36), and for homozygotes, 1.72 (CI 1.33-2.22). rheumatoid arthritis *rs6920220 [P= 2.6 x 10(-6), OR 1.22 (1.13-1.33)]. *rs5029937 *rs13207033 protective [P= 0.0001, OR 0.86 (0.8-0.93)] perfectly correlated with rs10499194 The combination of the carriage of both risk alleles of rs6920220 and rs5029937 together with the absence of the protective allele of rs13207033 was strongly associated with RA when compared to carriage of none [OR of 1.86 (95% CI) (1.51-2.29)]. This equates to an effect size of 1.50 (95% CI 1.21-1.85) Lack of association or interactions between the IL-4, IL-4Ralpha an...
complex; generally greater risk for cancer progression
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rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and H131R. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...
Magnitude: 1.1
Frequency: 91.8%
Repute:Bad
References:100
Frequency: 91.8%
Repute:Bad
References:100
Normal, but higher risk for certain autoimmune diseases. Almost everyone has this form, but it indicates a slightly higher risk of Ankylosing Spondylitis, Crohn's Disease (1.09x), Psoriasis (1.06x), and Ulcerative Colitis (1.06x). The risk is much greater than for the rare version. This is the interleukin-23 (IL-23) receptor. Media:http://www.the-rheumatologist.org/details/article/2528901/Neutralizing_IL-23_and_Its_Targets_May_Improve_Ankylosing_Spondylitis.html] Neutralizing IL-23 and Its Targets May Improve Ankylosing Spondylitis by Lara C. Pullen, PhD in The Rheumatologist newsmagazine ]
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A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-1....
Frequency: 1.8%
References:5
References:5
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[OMIM:?] [GWAS:None]
1.7x increased risk for Crohn's disease
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rs2076756 is a SNP of the NOD2 gene found in a genome-wide association study to be associated with Crohn's disease. In several European populations, the minor NOD2 allele, rs2076756(G), is associated with increased risk for Crohn's disease. The odds ratio (pooled over several populations) is 1.71 (CI: 1.42-2.05, p=6x10<sup>-8</sup>). Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. Strategies and issues in the detection of pathway enrichment in genome-wide association studies. Detecting gene-gene interactions that underlie human diseases. Role of NOD1/CARD4 and NOD2/CARD15 gene polymorphisms in cancer etiology. [PharmGKB:C...
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[GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
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Strategies and issues in the detection of pathway enrichment in genome-wide association studies. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. Association of novel genetic Loci with circulating fibrinogen levels: a genome-wide association study in 6 population-based cohorts. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [OMIM:INFLAMMATORY BOWEL DISEASE 5; [[IBD5]]] [GWAS:Crohn's disease]
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[GWAS:Inflammatory bowel disease]
Frequency: 34.5%
References:2
References:2
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[GWAS:Inflammatory bowel disease]
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rs2227564 A functional polymorphism within plasminogen activator urokinase (PLAU) is associated with Alzheimer's disease . *rs2227564 distribution of four tagSNPs (rs2227562 in intron 5, rs2227564 in exon 6, rs2227571 in intron 9, and rs4065 in 3' UTR) in the PLAU gene in a large case-control study of Alzheimer's disease No association of a non-synonymous PLAU polymorphism with Alzheimer's disease and disease-related traits. Elevated amyloid beta protein (Abeta42) and late onset Alzheimer's disease are associated with single nucleotide polymorphisms in the urokinase-type plasminogen activator gene. Linkage disequilibrium patterns and tagSNP transferability among European populations. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disea...
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[GWAS:Inflammatory bowel disease]
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[OMIM:INFLAMMATORY BOWEL DISEASE 26; IBD26] [GWAS:None]
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[GWAS:Inflammatory bowel disease]
Frequency: 39.8%
References:1
References:1
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[GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
Frequency: 40.7%
References:2
References:2
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[GWAS:Inflammatory bowel disease]
Frequency: 40.7%
References:2
References:2
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[GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
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[GWAS:None]
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23andMe reports that the T allele of rs2155219 is associated with hay fever (allergic rhinitis) and allergy to grass pollen. [GWAS:None]
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via spitoon reports about which identifies 32 snps relevant to Crohn's disease: '''Out of a possible total of 46, 80% of people will have between 17 and 25 copies of the riskier versions of these SNPs. Because there are so many of these SNPs--and because the riskier versions are often more common than their less risky counterparts--even people at the high end of the distribution are not much more likely than average to develop Crohn's disease.''' *rs3197999 A 1.2 *rs2188962 T 1.25 *rs2476601 G 1.31 *rs2274910 C 1.14 *rs9286879 G 1.19 *rs10045431 C 1.11 *rs6908425 C 1.21 *rs2301436 T 1.21 *rs1456893 A 1.2 *rs1551398 A 1.08 *rs10758669 C 1.12 *rs3764147 G 1.25 *rs2872507 A 1.12 *rs744166 A 1.18 *rs762421 G 1.13 *rs3763313 C 1.19 Proxy snps on 23andMe *rs7714584 G 1.33 *rs6478108 T 1.22 *rs12...
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[GWAS:None]
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[GWAS:Inflammatory bowel disease]
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[PharmGKB:Non-Curated GWAS Results: Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease (Initial Sample Size: 1,011 cases, 4,250 controls; Replication Sample Size: 1,922 cases, 14,124 controls; Risk Allele: rs2315008-G). This variant is associated with Inflammatory bowel disease.] [OMIM:INFLAMMATORY BOWEL DISEASE 24; IBD24] [GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
possibly reduced risk for Crohn's disease
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the association may be specific to Crohn's disease, as opposed to all types of IBD. significant associations with rs1004819, rs7517847, and rs11209026. Having any CARD15 variant was associated with a significant risk for Crohn's disease (P < 0.0001). rs7517847 (P=4.9x10(-9), OR 0.65, 0.56-0.75), is statistically independent of rs11209026. Replicated reduced risk for Crohn's disease with the rs7517847(G) allele in a study of Italian patients, but not ulcerative colitis. Each incidence of the G allele was associated with a decrease in Crohn's Disease in New Zealand populations studied. Investigation of the IL23R gene in a Spanish rheumatoid arthritis cohort. rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and O...
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[GWAS:Inflammatory bowel disease]
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[GWAS:None]
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[GWAS:Inflammatory bowel disease]
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TNFSF15 is an ethnic-specific IBD gene. IBD-associated TL1A gene (TNFSF15) haplotypes determine increased expression of TL1A protein. Strategies and issues in the detection of pathway enrichment in genome-wide association studies. Comprehensive linkage and association analyses identify haplotype, near to the TNFSF15 gene, significantly associated with spondyloarthritis. Identifying and testing candidate genetic polymorphisms in the irritable bowel syndrome (IBS): association with TNFSF15 and TNFalpha [OMIM:INFLAMMATORY BOWEL DISEASE 16; IBD16] [GWAS:Inflammatory bowel disease]
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[GWAS:None]
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[GWAS:Inflammatory bowel disease]
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A genome-wide association study of metabolic traits found that variations in rs281408 are strongly correlated with fucose levels in urine samples, which in turn are associated with inflammatory bowel disease and Crohn’s disease. This single nucleotide polymorphism is specifically found in the RASIP1 gene, with reference allele C and minor allele A (P = 9.5x10-27). RASIP1 is positioned within a large linkage-desequilibrium-block on chromosome 19 also encompassing FUT2 and IZUMO1. As such, rs281408 has a strong LD with rs492602 (r2 = 0.87), which is located within the FUT2 gene that encodes for fucosyltransferase. FUT2 has previously been associated with vitamin B12 levels in the serum . The FUT2 gene product is integral for secretion and display of ABO blood group antigens on mucosal ...
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[GWAS:Inflammatory bowel disease]
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[PharmGKB:Non-Curated GWAS results: Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease (Initial Sample Size: 1,011 cases, 4,250 controls; Replication Sample Size: 1,922 cases, 14,124 controls). This variant is associated with Inflammatory bowel disease.] [OMIM:INFLAMMATORY BOWEL DISEASE 25; IBD25] [GWAS:None] [GWAS:Inflammatory bowel disease]
Frequency: 51.8%
References:14
References:14
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[GWAS:Crohn's disease]
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Conditional analysis of the major histocompatibility complex in rheumatoid arthritis. Identifying rheumatoid arthritis susceptibility genes using high-dimensional methods. The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. [OMIM:?] [GWAS:None]
Frequency: 57.5%
Repute:Bad
References:11
Repute:Bad
References:11
1.2x risk
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rs10761659 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.23 (CI 1.05-1.45), and for homozygotes, 1.55 (CI 1.3-1.84). [OMIM:INFLAMMATORY BOWEL DISEASE 15; IBD15] [GWAS:None]
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[GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
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[GWAS:None]
Frequency: 64.6%
References:2
References:2
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[GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
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[GWAS:Inflammatory bowel disease]
Frequency: 70.8%
References:2
References:2
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[GWAS:None]
Frequency: 72.6%
References:1
References:1
(hide)
[GWAS:Inflammatory bowel disease]
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[GWAS:None]
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[GWAS:Inflammatory bowel disease]
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linked to Crohn's disease and type-1 diabetes Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants. Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1). The expanding genetic overlap between multiple sclerosis and type I diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1. Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cyto...
Frequency: 82.3%
References:1
References:1
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[GWAS:Inflammatory bowel disease]
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[GWAS:None]
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Newly identified genetic risk variants for celiac disease related to the immune response. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. Shared and distinct genetic variants in type 1 diabetes and celiac disease. Association study of the IL18RAP locus in three European populations with coeliac disease. Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associatio...
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[PharmGKB:Non-Curated Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. (Initial Sample Size: 1,167 cases, 777 controls; Replication Sample Size: 1,855 cases, 3,091 controls); (Region: 1q32.1; Reported Gene: IL10; Risk Allele: rs3024505-T) This variant is associated with Ulcerative colitis.] [OMIM:INFLAMMATORY BOWEL DISEASE 23; IBD23] [GWAS:Ulcerative colitis]
60 snps
(hide) Intracranial Aneurysm
Magnitude: 2
Frequency: 50.0%
Repute:Bad
References:77
Frequency: 50.0%
Repute:Bad
References:77
1.3x risk for Heart Attack. Normal risk for Abdominal Aortic Aneurysm and Brain Aneurysm. One copy of an SNP that increases risk of Myocardial Infarction (Heart Attack) and other Coronary Heart Disease. It has been shown that regularly eating raw vegetables and fruit can reduce the risk to the same level as people without this SNP. This SNP also has the normal medium risk of abdominal aortic aneurysm (weakened artery to abdomen and legs) or brain aneurysm (weakened artery to brain).
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This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...
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The presence of an rs173686(C) allele has been linked to increased risk of a certain type of stroke, Intracranial Aneurysm, in a population of Dutch adults. A study of 240 Chinese Han nationality patients with at least one intracranial aneurysm and matched controls did not replicate this result. Note: the dbSNP sequence entry for this SNP represents the noncoding strand, and is thus the reverse complement compared to the SNP as referred to in .
2 snps
(hide) Intrahepatic cholestasis of pregnancy
1.7x higher risk for intrahepatic cholestasis of pregnancy
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rs2287622 is a SNP in the ATP-binding cassette, sub-family B (MDR/TAP), member 11 ABCB11 gene. The more common (T) allele encodes a Val, while the rarer (C) allele encodes a Ala; this SNP is also known as V444A or c.1331T>C. In two intrahepatic cholestasis of pregnancy (ICP) cohorts (333 UK, 158 continental Europe), rs2287622 was associated with ICP (allelic odds ratio for C vs T 1.7 (CI: 1.4-2.1, p<0.0001). In addition, (C;C) homozygotes were more likely to have ICP than (T;T) homozygotes with and odds ratio of 2.8, (CI 1.7-4.4, p<0.0001).
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
2 snps
(hide) Ischemia
normal
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rs4673, also known as C242T or H72Y, is a SNP in the NAD(P)H oxidase p22(phox) subunit CYBA gene. A study of German patients with ischemic stroke or transient ischemic attack under the age of 50 (n = 161) concluded that rs4673(T;T) individuals were almost 4 times more likely to experience cerebral ischemia (odds ratio 3.85, CI: 1.39-10.64) compared to rs4673(C;T) or (C;C) individuals after adjusting for classical risk factors. A meta-analysis concluded that the T allele effect may vary between ethnicities in both direction of effect and significance; Asian populations may have reduced coronary artery disease risk associated with the T allele. Genetic polymorphisms and susceptibility to lung disease. Genetic association of glutathione peroxidase-1 with coronary artery calcification in type ...
1 snp
(hide) Kawasaki disease
Frequency: 38.1%
References:25
References:25
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Associated with systemic lupus erythematosus (SLE) [PharmGKB:Non-Curated GWAS Results: Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX (Initial Sample Size: 1,311 cases, 3,340 controls; Replication Sample Size: 793 cases, 857 controls; Risk Allele: rs13277113-A).] [OMIM:FAMILY WITH SEQUENCE SIMILARITY 167, MEMBER A; FAM167A] [GWAS:Systemic lupus erythematosus] [GWAS:Systemic lupus erythematosus]
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[OMIM:?] [GWAS:Rheumatoid arthritis]
Frequency: 52.3%
References:4
References:4
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plos rs17531088 and rs7199343 associated with Kawasaki disease [PharmGKB:Non-Curated GWAS results: A genome-wide association study identifies novel and functionally related susceptibility loci for Kawasaki disease. (Initial Sample Size: 107 cases, 134 controls; Replication Sample Size: 583 cases, 1,357 family members); (Region: 3q26.31; Reported Gene(s): NAALADL2; Risk Allele: rs17531088-T); (p-value= 0.000001).This variant is associated with Kawasaki disease.] [GWAS:Kawasaki disease]
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Conditional analysis of the major histocompatibility complex in rheumatoid arthritis. Identifying rheumatoid arthritis susceptibility genes using high-dimensional methods. The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. [OMIM:?] [GWAS:None]
4 snps
(hide) Kidney stones
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This SNP is reportedly associated with chronic kidney disease and kidney stones. [GWAS:None]
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DeCode reports that carriers of two T alleles at rs219778 have a slightly increased risk of developing kidney stones.
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23andMe blog each G at rs4293393 decreased the odds of chronic kidney disease by 24%. Approximately 18% of people with European ancestry have at least one G at this SNP. DeCode reports that the T allele of rs4293393 is associated with kidney stones and chronic kidney disease. This SNP may also be associated with susceptibility to gout], hypertension, and diabetes.
common in complete genomics
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[PharmGKB:Curated One study at 115 subjects with pancreatitis and 66 controls found that the CASR R990G variant is a significant risk factor for chronic pancreatitis.]
6 snps
(hide) Lactose intolerance
probably able to digest milk
77% of Europeans with this are able to digest lactose and dairy products. People without this are more likely to experience lactose intolerance.
can digest milk
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Also known as 'C/T(-13910)', and located in the MCM6 gene but with influence on the lactase LCT gene, rs4988235 is one of two SNPs that is associated with the primary haplotype associated with hypolactasia, more commonly known as lactose intolerance in European Caucasian populations. , In these populations, the rs4988235(T) allele is both the more common allele and the one associated with lactase persistence; individuals who are rs4988235(C;C) are likely to be lactose intolerant. In populations of sub-Saharan Africans, though, the rs4988235(T) allele is so rare that it's unlikely to be predictive of lactase persistence, and other SNPs are predictive instead. * See also OMIM 601806.0001 Measuring European population stratification with microarray genotype data. Adult-type hypolactasia is no...
Can digest milk.
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Also known as 'G/A(-22018)' and located in the MCM6 but with influence on the lactase LCT gene, rs182549 is one of two SNPs that is associated with the primary haplotype associated with hypolactasia, more commonly known as lactose intolerance in European Caucasian populations. In these populations, the rs182549(C) allele (as named in accordance with dbSNP) is both the more common allele and the one associated with lactose intolerance. In populations of sub-Saharan Africans, though, the rs182549(C) allele is unlikely to be predictive of lactose intolerance, and other SNPs are predictive instead. * See also OMIM 601806.0002 Gender differences in genetic risk profiles for cardiovascular disease. Natriuretic peptide system gene variants are associated with ventricular dysfunction after coronar...
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in complete genomics
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Some news linked it to lactose intolerance: * Screening of variants for lactase persistence/non-persistence in populations from South Africa and Ghana. * Association of the European lactase persistence variant (LCT-13910 C>T polymorphism) with obesity in the Canary Islands. * Several different lactase persistence associated alleles and high diversity of the lactase gene in the admixed Brazilian population. It is however a typo: “There was a typographical error in the rs number in the Abstract and Introduction. The correct rs number is rs4988235.”[http://www.plosone.org/annotation/listThread.action?root=58349]
1 genoset 5 snps
(hide) LDL cholesterol
1.2x risk of coronary artery disease
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rs599839 and rs4970834 explain about 1% of the variation in circulating LDL-cholesterol levels. 'When we look at this particular genetic variance, of all the cholesterol variation among the population, 1% of it can be attributed to this particular locus,' said Sandhu. 'This is equivalent to more established genes for LDL regulation, particularly APOE.' rs646776 also linked. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins found each minor allele to increase statin effectiveness by 1.3% (rs646776, β=−0.013, s.e.=0.002, P=1.05 × 10−9 and rs12740374, β=−0.013, s.e.=0.002, P=1.05 × 10−9). 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs1746...
Slightly lower odds of developing CHD.
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[PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of LDL-C and apolipoprotein B. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): LDL-C: p = 5.2 x 10 (-15);ApoB: p = 7.0 x 10(-18). Type of association: CO; GN] [OMIM:?] [GWAS:LDL cholesterol]
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased LDL cholesterol, increased HDL cholesterol and increased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [Pharm...
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per the 23andMe blog, the minor allele of this SNP (A) was associated with increased LDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Common variants at 30 loc...
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[PharmGKB:Non-Curated GWAS results: Common SNPs in HMGCR in Micronesians and Whites Associated With LDL-Cholesterol Levels Affect Alternative Splicing of Exon13. (Initial Sample Size: 2,346 Micronesian individuals; Replication Sample Size: 1,464 European white cases, 1,467 European white controls); (Region: 5q13.3; Reported Gene(s): HMGCR; Risk Allele: rs7703051-A); (p-value= 0.00000001).This variant is associated with LDL cholesterol.] [GWAS:LDL cholesterol]
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LDL cholesterol levels being the quantitative trait associated with in Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. The HMG-CoA reductase gene and lipid and lipoprotein levels: the multi-ethnic study of atherosclerosis. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. The role of HMGCR alternative splicing in statin efficacy. [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 5q13.3; Reported Gene(s): HMGCR; Risk Allele: rs3846663-T); (p-value= 0.000000000008).This variant is associated ...
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[GWAS:LDL cholesterol]
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[GWAS:LDL cholesterol]
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[GWAS:LDL cholesterol]
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Genome-wide association study of plasma polyunsaturated fatty acids in the InCHIANTI Study. Genetic determinants of circulating sphingolipid concentrations in European populations. Single nucleotide polymorphisms in the FADS gene cluster are associated with delta-5 and delta-6 desaturase activities estimated by serum fatty acid ratios. FADS genetic variants and omega-6 polyunsaturated fatty acid metabolism in a homogeneous island population. Genetic variation in lipid desaturases and its impact on the development of human disease. Genetic variation of the FADS1 FADS2 gene cluster and n-6 PUFA composition in erythrocyte membranes in the European Prospective Investigation into Cancer and Nutrition-Potsdam study. FADS1 genetic variability interacts with dietary alpha-linolenic acid intake to ...
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}}per the 23andMe blog, the minor allele of this SNP (T) was associated with increased LDL cholesterol {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} Analysis of recently identified dyslipidemia alleles reveals...
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[GWAS:C-reactive protein]
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The G allele of this SNP in the TOMM40 gene may be associated with late-onset Alzheimer's disease. Association of ApoE genetic variants with obstructive sleep apnea in children. Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. A genome-wide association study for late-onset Alzheimer's disease using DNA pooling. Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease. Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Genome-wid...
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gwas among adults residing on Korcula Island in Croatia, LDL cholesterol, the A allele associated with lower LDL cholesterol<br><br> [PharmGKB:Non-Curated GWAS results: Genome-wide association study of biochemical traits in Korcula Island, Croatia. (Initial Sample Size: 898 individuals; Replication Sample Size: NR); (Region: 12q24.23; Reported Gene(s): KSR2; Risk Allele: rs4767631-A); (p-value= 0.0000006).This variant is associated with Biochemical measures.] [GWAS:Biochemical measures]
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[GWAS:None]
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[GWAS:LDL cholesterol]
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LDL cholesterol and total cholesterol levels being the quantitative trait associated with in [GWAS:Quantitative traits]
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[PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 20q12; Reported Gene(s): MAFB; Risk Allele: rs6102059-T); (p-value= 0.000000004).This variant is associated with LDL cholesterol.] [GWAS:LDL cholesterol]
Frequency: 50.8%
References:15
References:15
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Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins found each minor allele to increase statin effectiveness by 1.3% (rs646776, β=−0.013, s.e.=0.002, P=1.05 × 10−9 and rs12740374, β=−0.013, s.e.=0.002, P=1.05 × 10−9). [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 1p13.3; Reported Gene(s): CELSR2, PSRC1, SORT1; Risk Allele: rs12740374-T); (p-value= 2E-42).This variant is associated with LDL cholesterol.] [OMIM:SORTILIN; SORT1] [GWAS:LDL cholesterol]
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[PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,589 individuals; Replication Sample Size: 7,440-10,783 individuals; Risk Allele: rs2254287-G). This variant is associated with LDL cholesterol levels.] [GWAS:LDL cholesterol]
elevated lipids
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rs693 increases susceptibility to Elevated Apolipoprotein B and LDL-Cholesterol for carriers of the T allele [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 2p24.1; Reported Gene(s): APOB; Risk Allele: rs693-G); (p-value= 0.00000000000000004).This variant is associated with LDL cholesterol.] [OMIM:APOLIPOPROTEIN B; APOB] [GWAS:Cholesterol, total]
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gwas among adults residing on Korcula Island in Croatia, cholesterol, the G allele associated with increased total cholesterol and increased LDL cholesterol<br><br> [PharmGKB:Non-Curated GWAS results: Genome-wide association study of biochemical traits in Korcula Island, Croatia. (Initial Sample Size: 898 individuals; Replication Sample Size: NR); (Region: 21q22.3; Reported Gene(s): PKNOX1; Risk Allele: rs2839619-G); (p-value= 0.000008).This variant is associated with Biochemical measures.] [GWAS:Biochemical measures]
1.29x increased risk for heart disease
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rs599839 is a SNP found to be associated with heart disease by the German MI (Myocardial infarction) Family Study group, over several populations. The odds ratio for the (common) risk allele, rs599839(A), is 1.29 (CI: 1.18-1.40, adjusted p=0.0006). rs599839 and rs4970834 explain about 1% of the variation in circulating LDL-cholesterol levels. 'When we look at this particular genetic variance, of all the cholesterol variation among the population, 1% of it can be attributed to this particular locus,' said Sandhu. 'This is equivalent to more established genes for LDL regulation, particularly APOE.' Another study also reports an association between rs599839(A) and higher LDL levels, in over 4,000 Caucasian Europeans. In one study, the (A) allele is associated with a 6% increase in nonfasting ...
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[GWAS:LDL cholesterol]
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[GWAS:LDL cholesterol]
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[GWAS:LDL cholesterol]
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[PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 2p24.1; Reported Gene(s): APOB; Risk Allele: rs515135-T); (p-value= 5E-29).This variant is associated with LDL cholesterol.] [GWAS:LDL cholesterol]
normal
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The ancestral allele is C. The rs7412(T) allele, also known as Arg176Cys, generally indicates the presence of an Apoε2 allele; see the ApoE page for a full discussion of the ApoE alleles and their association with Alzheimer's disease. Another SNP related to ApoE is rs429358. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs7412(C) allele were more likely to gain significant weight compared to rs7412(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs4765623, were also significantly associated with weight profiles in these patients. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity ...
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[PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 5q33.3; Reported Gene(s): TIMD4, HAVCR1; Risk Allele: rs1501908-G); (p-value= 0.00000000001).This variant is associated with LDL cholesterol.] [GWAS:LDL cholesterol]
average
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rs780094, a SNP in the GCKR gene encoding the glucokinase regulatory protein, contributes to the risk of type-2 diabetes and dyslipidaemia in mulitple populations. The effect on type 2 diabetes is probably mediated through impaired beta cell function rather than through obesity. The rs780094(A) risk allele is associated with the following traits : * higher levels of fasting serum triacylglycerol * impaired fasting and OGTT-related insulin release * dyslipidemia * somewhat reduced risk of type-2 diabetes There may also be an additive effect between this SNP and a SNP known as 'GCK -30A', rs1799884, at least on fasting serum insulin levels. rs780094 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched norm...
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T allele is associated with 3.47mg/dl increase in HDL cholesterol (good cholesterol). [PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of HDL-C and apolipoprotein A1. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): HDL-C: p = 1.0 x 10 (-41);ApoA1: p = 1.1 x 10(-34). Type of association: CO; GN] [OMIM:?] [GWAS:HDL cholesterol]
Normal/Average risk for Alzheimer's
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Apolipoprotein E ApoE status is technically defined by two different SNPs, rs429358 and rs7412. This SNP, rs4420638, is situated about 14kb away in the adjacent ApoC1 gene and is co-inherited with ApoE and thus associated with late-onset Alzheimer's disease. rs4420638 (the proxy SNP) is not independent of rs429358. These two SNPs are correlated with each other and it's believed that most of the association with AD at rs4420638 is due to its proximity to rs429358. That said, rs4420638 is not a perfect proxy for rs429358 either -- rs4420638 correlates better for certain genotypes and for certain ethnicities. For example, if you have the genotype at rs4420638 that is more correlated with the e4 allele of APOE, you still only have a 50% chance of actually having the e4 allele. And rs4420638 is...
Magnitude: 0
Frequency: 69.0%
References:14
Frequency: 69.0%
References:14
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23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 Genetic susceptibility to coronary heart disease in type 2 diabetes: 3 independent studies. Genetics of diabetes complications. Using a latent growth curve model for an integrative assessment of the effects of genetic and environmental factors on multiple phenotypes. Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoids: a genome-wide association study. Genetics of coronary artery disease: focus on genome-wide association studies. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to...
Magnitude: 0
Frequency: 82.0%
Repute:Good
References:18
Frequency: 82.0%
Repute:Good
References:18
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,589 individuals; Replication Sample Size: 7,440-10,783 individuals; Risk Allele: rs16996148-G). This variant is associated with LDL cholesterol levels.] [GWAS:LDL cholesterol] [GWAS:Triglycerides]
common on affy axiom data
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased LDL cholesterol, increased HDL, and decreased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Cur...
common on affy axiom data
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per the 23andMe blog, the minor allele of this SNP (A) was associated with increased LDL cholesterol (wrong allele listed on the 23andMe blog) {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || A || + || || |- |} [PharmGKB:Non-Curat...
Magnitude: 0
Frequency: 98.2%
Repute:Bad
References:19
Frequency: 98.2%
Repute:Bad
References:19
normal Since the rare geno is good, this can be considered slightly bad
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rs11591147, also known as R46L, is a SNP in the PCSK9 gene. As early as 2006, the minor rs11591147(T) allele was reported to be associated with lower LDL cholesterol levels, and most studies since have found that this also correlates to a two to three fold reduced risk for both early- and late-onset cardiovascular events and disease. As part of a 9 SNP set studied in a meta-analysis totaling over 300,000 patients, rs11591147 was the SNP with the greatest effect on LDL-C and therefore cardiovascular risk reduction. The set of SNPs was as follows, ordered from strongest to least effect on coronary risk, and the allele shown is the one associated with reduced LDL-C levels along with the associated (or nearby) lipid metabolism gene: * rs11591147(T), PCSK9 * rs4420638(A), APOE * rs6511720(T), L...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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[GWAS:LDL cholesterol]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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rs28362286, also known as C679X, is a SNP in the PCSK9 gene. It has been reported in several studies (including ) to be both rare (2% frequency in Africans, 0.1% in Europeans) and as a dominant nonsense mutation a cause of plasma LDL-C levels being up to 40% lower than average. This lowered LDL-C level is thought to be directly associated with very significantly lowered risk for coronary events. 23andMe blog The T version of rs11591147 and the A version of rs28362286 have both been associated with decreased LDL levels. Each copy of these variants leads to lower LDL cholesterol. Longitudinal association of PCSK9 sequence variations with low-density lipoprotein cholesterol levels: the Coronary Artery Risk Development in Young Adults Study. [OMIM:LOW DENSITY LIPOPROTEIN CHOLESTEROL, LOW PLAS...
40 snps
(hide) Left
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having minor alleles at all 3 of rs1446109-rs1007371-rs723524 may affect left-right asymmetrical brain function, such as handedness, and much of human cognition, behavior and emotion. pdf full paper
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having minor alleles at all 3 of rs1446109-rs1007371-rs723524 may affect left-right asymmetrical brain function, such as handedness, and much of human cognition, behavior and emotion. pdf full paper Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry.
common allele on the minus strand
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having minor alleles at all 3 of rs1446109-rs1007371-rs723524 may affect left-right asymmetrical brain function, such as handedness, and much of human cognition, behavior and emotion. pdf full paper
3 snps
(hide) Leprosy
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Variant in the CCDC122 region associated with increased susceptibility to leprosy in Asians, according to the 23andMe blog 23andMe's blog. The risk allele is A, and the odds ratio is 1.52. [OMIM:?]
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[GWAS:Leprosy]
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Variant in the RIPK2 gene associated with a reduced risk of leprosy in Asians, according to the 23andMe blog. The protective allele is A, and the odds ratio is 0.76. Leprosy Susceptibility [GWAS:Leprosy]
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Associated with increased risk for Crohn's disease in a study of 380 Korean patients. This SNP is associated with greater susceptibility to leprosy in Asians, according to the 23andMe blog. The risk allele is T, and the odds ratio is 1.37. The TNFSF15 gene encodes a cytokine protein in the tumor necrosis factor (TNF) family. TNFSF15 is an ethnic-specific IBD gene. Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. TNFSF15 polymorphisms are associated with susceptibility to inflammatory bowel disease in a new European cohort. IBD-associated TL1A gene (TNFSF15) haplotypes determine increased expression of TL1A protein. Comprehensive linkage and association analyses identify haplotype, near to the TNFSF15 gene, significantly associated with spondyloarthrit...
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Variant in the NOD2 gene associated with greater susceptibility to leprosy in Asians, according to the 23andMe blog. The risk allele is C, and the odds ratio is 1.59. Another gene associated with susceptibility to leprosy is TNFSF15. SNPs in both the NOD2 and TNFSF15 genes are also associated with susceptibility to Crohn's disease. Leprosy Susceptibility [GWAS:Leprosy]
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Variant in the C13orf31 region associated with increased susceptibility to leprosy, according to the 23andMe blog 23andMe blog. The risk allele is G, and the odds ratio is 1.68. Other genes associated with both Crohn's disease and leprosy include NOD2 and TNFSF15, according to 23andMe's blog. Leprosy Susceptibility [PharmGKB:Non-Curated GWAS Results: Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease (Initial Sample Size: 3,230 cases 4,829 controls; Replication Sample Size: 2,325 cases 1,809 controls 1,339 affected trios; Risk Allele: rs3764147-G).] [OMIM:?] [GWAS:Leprosy] [GWAS:Crohn's disease]
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[PharmGKB:Curated The genotype distributions for the I602S variant in the TLR-1 gene differed significantly between patients with mild malaria and persons with asymptomatic infection. The 602S allele was associated with an odds ratio (OR) of 2.2 (P= .003) for malaria among patients with mild malaria.] [OMIM:TOLL-LIKE RECEPTOR 1; TLR1]
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
8 snps
(hide) Leukemia
~1.5x increased risk for chronic lymphocytic leukemia
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rs872071 is a SNP associated with the interferon regulatory factor 4 IRF4 gene. In a GWAS study including over 1,500 Caucasian patients with chronic lymphocytic leukemia (CLL), the rs872071(G) allele showed the strongest association (p = 1.91 x 10e-20) of all SNPs studied. The reported odds ratio was 1.54. See also: 23andMe blog A subsequent study () has found a similar association extending to another 800+ Spanish and Swedish CLL patients. rs872071 was also seen to be associated with CLL in Hong Kong Chinese (71 patients), with a reported odds ratio of 1.78 (CI: 1.25-2.53). A related hematologic malignancy, Hodgkin's lymphoma, may also be influenced by rs872071. Two case-control series totalling 529 and 2192 patients found an odds ratio of 1.21 (CI: 1.05-1.39, p = 0.009). [PharmGKB:Non-C...
Frequency: 36.9%
References:9
References:9
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23andMe blog chronic lymphocytic leukemia *rs13397985 G 1.41 [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs13397985-G). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
Frequency: 39.3%
References:6
References:6
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23andMe blog chronic lymphocytic leukemia *rs11083846 A 1.35 [GWAS:Chronic lymphocytic leukemia]
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23andMe blog chronic lymphocytic leukemia *rs7176508 A 1.37 [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs7176508-A). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
Frequency: 64.2%
References:5
References:5
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23andMe blog chronic lymphocytic leukemia *rs17483466 G 1.39 Genetic susceptibility for chronic lymphocytic leukemia among Chinese in Hong Kong. [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs17483466-G). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
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chronic lymphocytic leukemia rs2266690 rs17028658 rs4505265 rs1045485 rs2779251 rs3136687 Influence of the inducible nitric oxide synthase gene (NOS2A) on inflammatory bowel disease susceptibility.
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Leukemia [GWAS:Chronic lymphocytic leukemia]
common in clinvar
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rs1800566 (C609T, Pro187Ser) is a snp within NQO1 (NAD(P)H dehydrogenase (quinone 1)). A Ser (T) at this location denotes the NQO1*2 allele. influences the risk of breast cancer according to the 23andMe blog rs1800566 increases susceptibility to Lung cancer 0.48 times for heterozygotes (CT) [PharmGKB:Curated Risk or phenotype-associated allele: C/T. Phenotype: There was no association between the NQO1*2 polymorphism and the risk of anthracycline-related CHF. Study size: 145. Study population/ethnicity: Nested case-control study was conducted within a cohort of 1979 patients enrolled in the Childhood Cancer Survivor Study who received treatment with anthracyclines and had available DNA. Significance metric(s): OR = 1.04; p = 0.97. Type of association: CO; TOX; ADR.] [OMIM:NAD(P)H DEHYDROGE...
common on affy axiom data
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23andMe blog chronic lymphocytic leukemia *rs735665 A 1.45 news Slager and colleagues validated these in an independent sample of patients. The strongest association was for rs735665 on 11q24, where the risk was 50 percent higher. This was closely followed by a 39 percent increased risk associated with rs9378805 on 6p25. Genetic variants at 6p21.33 are associated with susceptibility to follicular lymphoma. Genetic susceptibility for chronic lymphocytic leukemia among Chinese in Hong Kong. [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs735665-A). This variant is associated with Chronic ...
Magnitude: 0
Frequency: 87.6%
Repute:Good
References:3
Frequency: 87.6%
Repute:Good
References:3
common in complete genomics
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news Leukemia [PharmGKB:Curated GWAS results: Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemia. (Initial Sample Size: 487 children; Replication Sample Size: NR); (Region: 4q31.21; Reported Gene(s): IL15; Risk Allele: rs17007695-C); (p-value= 0.0000009).This variant is associated with Treatment response for acute lymphoblastic leukemia.] [GWAS:Treatment response for acute lymphoblastic leukemia]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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[OMIM:?]
but the rare allele is protective
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rs1045485, also known as D302H, is a SNP in the caspase-8 CASP8 gene. Several large studies indicate that the (C) allele of this SNP, located in exon 10 of the CASP8 gene, may reduce the risk of breast cancer in a dose dependent manner. The odds ratio is 0.89 for (C;G) and 0.74 for (C;C) carriers. article cancergenetics A 4-SNP haplotype including rs1045485 was significantly associated with breast cancer in a large European study (3,000+ cases, 3,000+ controls), with a per allele odds ratio of 1.3 (CI:1.12-1.49). chronic lymphocytic leukemia rs2266690 rs17028658 rs4505265 rs1045485 rs2779251 rs3136687 showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer No association seen between ...
13 snps
(hide) Li-Fraumeni syndrome
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:4
Frequency: 100.0%
Repute:Good
References:4
common in clinvar
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rs11540652, also known as Arg248Gln or R248Q, is a SNP in the p53 TP53 tumor suppressor gene. The rare rs11540652(A) allele is associated with predisposition to cancer in the form of Li-Fraumeni syndrome 1. This mutation is consistently denoted as pathogenic (causal) in ClinVar; see also OMIM 191170.0010. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. [OMIM:LI-FRAUMENI SYNDROME 1]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs28934574, also known as Arg282Trp or R282W, is a SNP in the p53 TP53 tumor suppressor gene. The rare rs28934574(T) allele is associated with predisposition to cancer in the form of a condition denoted Li-Fraumeni syndrome-like in OMIM. However, there is conflicting evidence in ClinVar as to whether this really is a pathogenic (causal) variant; some submitters indicate is benign while others say it is indeed pathogenic. See also OMIM 191170.0018 This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. [OMIM:OSTEOSARCOMA]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs28934576, also known as Arg273His or R273H, is a SNP in the p53 TP53 tumor suppressor gene. The minor allele is denoted as pathogenic (causal) in ClinVar. The rare rs28934576(A) allele is associated with predisposition to cancer in the form of Li-Fraumeni syndrome 1. Germline p53 Mutation in a Case of Li-Fraumeni Syndrome Presenting Gastric Cancer. A germline missense mutation CGT (Arg, wild type) to CAT (His) substitution at codon 273 of the p53 gene, causing Li-Fraumeni Syndrome with a gastric cancer in a Japanese. PCR direct sequencing analysis revealed a germline missense mutation in exon 8, causing a substitution of CAT (His) for CGT (Arg). See also OMIM 191170.20 This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencin...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs28934573, also known as Met133Thr or M133T, is a SNP in the p53 TP53 tumor suppressor gene. The rare rs28934573(C) allele is associated with predisposition to cancer in the form of Li-Fraumeni syndrome 1. This allele is considered pathogenic (causal) in ClinVar; see also OMIM 191170.0011. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. [OMIM:LI-FRAUMENI SYNDROME 1]
common in clinvar
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rs28934875, also known as Ala138Pro or A138P, is a SNP in the p53 TP53 tumor suppressor gene. The rare rs28934875(C) allele is associated with predisposition to cancer in the form of Li-Fraumeni syndrome 1. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. [OMIM:LI-FRAUMENI SYNDROME 1]
6 snps
(hide) Liver cancer
1.6x increased risk for prostate cancer; also other cancers 1.4 times as likely to develop colorectal cancer
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. This SNP has also been reported to influence the cancer-risk-decreasing effect of aspirin. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neig...
3.5x risk of hep-cancer in cirrhosis patients; higher glioma risk; 3x higher gallbladder cancer risk in females
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rs4444903 is a SNP, also known as +61, located in the promoter region of the epidermal growth factor EGF gene that influences the amount of EGF produced. The rs4444903(G) allele appears to produce higher amounts of EGF than the (A) allele. A study of 2 Caucasian populations of patients with alcoholic cirrhosis indicates that, for these patients, the presence of the risk allele rs4444903(G) increases the chances of developing hepatocellular carcinoma (liver cancer). After adjusting for age, sex, race, etiology, and severity of cirrhosis the number of (G) copies led to an odds ratio for either (G;G) or (A;G) genotypes versus the (A;A) genotype of 3.49 (CI: 1.29-9.44, p=.01). In another study, analysis of 197 glioma patients showed that the rs4444903(G) allele conferred higher risks for gliom...
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y or Cys282Tyr mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who act...
4 snps
(hide) Long QT syndrome
common in clinvar
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rs7626962, also known as Ser1103Tyr or S1103Y, is a SNP in the cardiac sodium channel SCN5A gene. Although relatively common (for a rare allele; 10 - 20% of individuals) in those of African ancestry, in all populations the rs7626962(T) allele has been reported to increase the risk for cardiac issues such as long QT syndrome but also arrhythmias and even sudden infant death syndrome. The odds ratio for displaying signs of arrhythmia for anyone carrying a rs7626962(T) allele is reported as 8.7 (CI 3.2 - 23.9) ; as for sudden infant death syndrome, at least in African-ancestry populations, the odds ratio for the same allele is reported as 4.9, leading to an odds ratio of 24 for rs7626962(T;T) homozygotes. This variant meets the criteria published in 2013 by the ACMG regarding incidental findi...
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
common in clinvar
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rs17221854, also known as Arg583Cys or R583C, is a SNP in the KCNQ1 gene on chromosome 11. The rs17221854(T) allele has been reported as associated with long QT syndrome. Additionally, a person who developed QT prolongation and torsade de pointes while taking the drug dofetilide carried this (T) allele, leading the authors to hypothesize that this mutation was responsible for the patient's drug response. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. [OMIM:LONG QT SYNDROME 1]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
common in clinvar
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rs41261344, also known as Arg1193Gln or R1193Q, is a SNP in cardiac sodium channel SCN5A gene. It is unclear how penetrant (causative) the rare allele of this SNP is for cardiac issues such as long QT syndrome. It was thought to be causative, based on observations in Caucasians, but then a report came out stating that 14% of Han Chinese carry this variant, most without any apparent problem. See OMIM and the GetEvidence summary below on right for more discussion. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. [OMIM:?]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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rs45546039, also known as Arg222Gln or R222Q, is a SNP in the cardiac sodium channel SCN5A gene. The rs45546039(A) allele is considered highly associated with dilated cardiomyopathy (CMD) and possibly long QT syndrome; see OMIM for discussion. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Ankyrin-B mutation causes type 4 long-QT cardiac arrhythmia and sudden cardiac death. A cardiac arrhythmia syndrome caused by loss of ankyrin-B function. Dysfunction in ankyrin-B-dependent ion channel and transporter targeting causes human sinus node disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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CAV3 gene mutation analysis in patients with idiopathic hyper-CK-emia. Mutant caveolin-3 induces persistent late sodium current and is associated with long-QT syndrome. Novel mechanism for sudden infant death syndrome: persistent late sodium current secondary to mutations in caveolin-3. Caveolin-3 T78M and T78K missense mutations lead to different phenotypes in vivo and in vitro. CAV3 gene mutation analysis in patients with idiopathic hyper-CK-emia. Mutant caveolin-3 induces persistent late sodium current and is associated with long-QT syndrome. Prevalence of long-QT syndrome gene variants in sudden infant death syndrome. Novel mechanism for sudden infant death syndrome: persistent late sodium current secondary to mutations in caveolin-3. Caveolin-3 T78M and T78K missense mutations lead to...
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
12 snps
(hide) Longevity
1.5x~2.7x more likely to live to 100. This is the best version of the well known longevity gene FOXO3. It greatly improves the odds of living to 100. It seems to improve insulin sensitivity, and reduce oxidative stress, among other things.
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A study of 5 genes in 3,741 Japanese men, some of whom lived significantly longer than average (centarians), concluded that the FOXO3 gene (also known as FOXO3A) harbors several SNPs linked to longevity, including this SNP, rs2802292, as well as rs2764264 and rs13217795. The odds ratio for rs2802292(G;G) vs (T;T) carriers was 2.75 (p = 0.00009; adjusted p = 0.00135). It is not known yet if this correlation is specific to Japanese males. This is discussed extensively at geneticfuture as a longevity snp. *(T) shorter lifespan *(G) longer lifespan Quoted from the geneticfuture article: 'No-one should consider this association to be definitive until it's been replicated in independent cohorts. Secondly, the effects of this variant are likely to differ between groups. According to the HapMap da...
2.5x risk for AMD; higher mortality among nonagenarians To minimize your risk of age related macular degeneration, consider a diet rich in vitamins C and E, lutein, zeaxanthin and the minerals zinc and copper, such as kale, spinach and broccoli. source
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rs1061170 is a SNP in the complement factor H CFH gene; it is also known as Tyr402His. The rs1061170(T) allele encodes the more common Tyr (Y), while the generally rarer rs1061170(C) encodes the His (H). This SNP has been associated primarily with age related macular degeneration, and to a lesser extent, with longevity. This research paper shows that CFH Y402H is the relevant mutation. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD. rs1061170 (aka Y402H 1277 T>C) was not associated with exudative AMD. CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese CFH variant rs1061170 Y402H is strongly associated with both dry and wet AMD rs1061170(C) alleles are significantly associa...
longer lifespan
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23andMe blog longevity rs2802288(A) increased the odds of living to 100 by 1.5x. rs2802288 is located very close to rs2802292 which was previously reported to have a similar effect.
greater odds of living to 95
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(C;C) greater odds of longevity Replication of an association of variation in the FOXO3A gene with human longevity using both case-control and longitudinal data. Association of the FOXO3A locus with extreme longevity in a southern Italian centenarian study.
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
better odds of living to 100
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This SNP may be related to longevity. One study found that Ashkenazi who lived to age 95 or older are more likely to have two copies of the C allele.
Faster aging. Increased risk for Dementia. Less good cholesterol. This reduces HDL ('good') cholesterol. HDL cholesterol removes cholesterol from artery walls and improves health. This SNP seems to be associated with higher blood pressure, less longevity, and more diseases of aging, in particular memory decline and dementia, and lower odds of living to 100, especially in Ashkenazi Jews. Attempting to raise HDL cholesterol may (or may not) be useful to mitigate the effects of this SNP.
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This SNP rs5882 in the CETP gene referred to as ILE405VAL and RSAI405V has been related to ageing and exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated...
Normal (higher) risk of physical impairment with age. This causes physical problems for older people, and Cerebral Small Vessel Disease in the brain.
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rs2811712 is a SNP associated with physical function in older individuals, and thus indirectly associated with longevity. In a study ultimately totaling over 3,300 elderly Caucasian individuals, the less common rs2811712(G) allele was associated with reduced physical impairment. Overall, severely limited physical function was present in 15.0% of the more common rs2811712(A;A) homozygotes, versus 7.0% of the rs2811712(G;G) homozygotes, yielding a per risk allele odds ratio of 1.48 (CI: 1.17-1.88, p=0.001). Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population. Consortium analysis of 7 candidate SNPs for ovarian cancer. Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer r...
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
Magnitude: 1.1
Repute:Bad
References:1
Repute:Bad
References:1
Less longevity for Ashkenazi Jewish women.
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rs34516635 is one of a small number of (rare) SNPs in the IGF1R gene found in a study of 384 Ashkenazi centenarians to potentially be associated with longevity and ageing. The rs34516635(A) allele was found somewhat more frequently (p=0.02) in female centenarians than in controls. No association was found for males. Higher IGF1 levels and an average decrease in maximal lifetime height of 2.5cm were also reported to be associated with (female Ashkenazi) centenarians.
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rs1935949 is an intronic SNP in the FOXO3 gene. rs1935949 demonstrated a significant association with longevity but only among women (odds ratio 1.35, CI:1.15-1.57, adjusted p=0.0093).
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rs3803304 is an intronic SNP in the AKT1 gene. rs3803304 was significantly associated with longevity in a meta-analysis across three cohorts (odds ratio 0.78, CI: 0.68-0.89, adjusted p=0.043).
normal
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rs1805097, also known as Gly1057Asp, is a SNP in the insulin receptor substrate-2 IRS2 gene. The rs1805097(G) allele is associated with the Gly, and the (A) allele with Asp. A longevity study categorizing 677 participants as either long-lived (i.e. over 85 years old) or not (less than 85) somehow concluded that rs1805097(A;A) individuals were about twice as likely to reach extreme old age (odds ratio 2.03, CI:1.39-2.99, p = .0003). [OMIM:DIABETES, TYPE II, SUSCEPTIBILITY TO]
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Based on a study of ~400 German centenarians (and matched controls), the more common rs1776180(C) allele is significantly enriched in female centenarians and may therefore be associated with longevity.
normal http://www.diygenomics.org/webapp/gen_data.php
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Located close to ApoE4, yet may independently (also) influence risk of Alzheimer's disease. A case-control study of 381 patients found a 2x higher risk for Alzheimer's disease associated with the rarer rs2075650(G) allele. This allele is associated with earlier onset of Alzheimer's disease, by ~7 years. (news) The data from this study are available online at The association of this SNP with late-onset Alzheimer's disease] was confirmed by a study reported in PLoS Genetics. The A allele of this SNP is one of 150 identified as relevant to exceptional longevity in Recent work suggests, however, that the linkage disequilibrium between rs2075650 and the ApoE ε4 defining SNP rs429358 means that there may be little, if any, independent effect of rs2075650 on Alzheimer's risk. rs2075650] was ...
common on affy axiom data
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The most significant SNP of 150 identified as relevant to exceptional longevity in ; the genotype statistically associated with a greater 'risk' of longevity is rs1036819(C;C). Newsweek has reported in the article The Little Flaw in the Longevity-Gene Study That Could Be a Big Problem that the associations for rs1036819 and rs1455311 may be incorrect because of a flaw in one of the chips used. Mentioned in retracted
17 snps
(hide) Lumbar disc disease
Back Pain: lower risk of Lumbar Disc Disease. This appears to reduce the risk of LDD, at least in Japanese people and women.
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The rs2073711 SNP (1184T→C ) is located in exon 8 of the cartilage intermediate layer protein gene (CILP). However, CILP gene is primarily known to be expressed abundantly in intervertebral discs, and was reported to have increased expression when degeneration occurs . For the rs2073711 SNP, the ancestral allele is T and the disease associated risk allele is C. A study of Asian patients with lumbar disc disease (LDD) implicates each copy of a (C) allele of SNP rs2073711 (as oriented with respect to dbSNP) as increasing risk about 1.6 fold. ==Background== Low back pain (LBP) is an enervating condition that affects 70-85% of all people during their lifetime . It can lead to decreased physical activity and quality of life, presenting considerable negative socioeconomic and health impact...
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Lumbar disc herniation (LDH), a form of lumbar disc disease, is one of the most common musculoskeletal diseases. rs1676486, a SNP also known as c.4603C-->T in the COLL11A1 gene (one of 3 Type XI collagen genes), has been implicated in a study of ~800 Japanese patients as being associated with LDH. The risk allele in dbSNP orientation is (A), and the odds ratio associated with the allele is 1.42 (CI: 1.23 - 1.65). [PharmGKB:Curated In independent Japanese populations, the T allele was shown to be associated with Lumbar Disc Herniation.] [OMIM:COLLAGEN, TYPE XI, ALPHA-1; COL11A1]
2 snps
(hide) Lung cancer
1.6x increased risk for prostate cancer; also other cancers 1.4 times as likely to develop colorectal cancer
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. This SNP has also been reported to influence the cancer-risk-decreasing effect of aspirin. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neig...
Magnitude: 3
Frequency: 15.9%
Repute:Bad
References:102
Frequency: 15.9%
Repute:Bad
References:102
higher risk for nicotine dependence, lower risk for cocaine dependence
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Associated with smoking phenotype (p=0.007) based on association study of 2,000+ individuals, and functional studies demonstrated that the risk allele decreased response to a nicotine agonist, therefore the rs16969968(A) allele is likely to be involved in nicotine dependence. In a study 500+ individuals with cocaine dependence, the same rs16969968(A) allele was associated with a 0.67x decreased risk (p = 0.0045). A study of 200 individuals replicated the association between this SNP and nicotine dependence, and also concluded that the rs16969968(A) allele was significantly associated with 'enhanced pleasurable responses' to a person's first cigarette. 23andMe blog 23andMe considers rs1051730 equivalent The association between rs16969968 and lung cancer may, in part, be confounded by chroni...
1.80x lung cancer risk; decreased response to alcohol
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23andMe blog rs8034191(C;C) decreased response to alcohol rs8034191 increases susceptibility to Lung cancer 1.27 times for heterozygotes (CT) and 1.80 times for homozygotes (CC) rs8034191 increases susceptibility to Lung cancer 1.28 times for heterozygotes (CT) and 1.81 times for homozygotes (CC) [PharmGKB:Non-Curated GWAS results: Familial Aggregation of Common Sequence Variants on 15q24-25.1 in Lung Cancer. (Initial Sample Size: 194 cases, 219 controls; Replication Sample Size: 3,878 cases, 4,831 controls); (Region: 15q25.1; Reported Gene(s): LOC123688, PSMA4, CHRNA3, CHRNA5, CHRNB4; Risk Allele: rs8034191-G); (p-value= 0.00000001).This variant is associated with Lung cancer.] [OMIM:LUNG CANCER SUSCEPTIBILITY 2; LNCR2] [GWAS:Lung cancer] [GWAS:Lung cancer]
1.8x increased risk of lung cancer; reduced response to alcohol, therefore possibly increased risk of alcohol abuse
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rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...
Magnitude: 2.5
Frequency: 20.0%
Repute:Bad
References:9
Frequency: 20.0%
Repute:Bad
References:9
1.28x lung cancer risk
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rs17487223 increases susceptibility to Lung cancer 1.28 times for carriers of the T allele plos Risk Factors for Age-Dependent Nicotine Addiction
Higher risk for number of cancers
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600+ Korean lung cancer patients were part of a study that concluded that the rs664143(T) allele, as oriented vis-a-vis dbSNP, located in the ATM gene and also known as IVS62+60G>A, was associated with increased risk, with an odds ratio of 1.68 (CI: 1.1-2.1, p<0.05). In a study of 119 American patients with potentially resectable pancreatic cancer, the rs664143(C) allele was associated with poorer overall survival (ie response) to combined gerncitabine radiation therapy. Also, as 1 of 3 SNPs its risk allele is associated with poorer overall survival for pancreatic cancer patients being treated with combined gerncitabine radiation therapy; median overall survival times of 31.0, 16.2, and 10.5 months were calculated for pancreatic cancer patients carrying < or = 1, 2, and 3 risk all...
Increased risk of lung cancer in non-smokers and never smokers
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news increased risk of lung cancer in non smokers. Analysis showed that the presence of this variant significantly increased the risk of a never smoker having lung cancer by 1.46 times (odds ratio 1.46, 95% confidence interval 1.26 to 1.70). [PharmGKB:Curated Risk or phenotype-associated allele: Not specified. Phenotype: This variant was asssociated with risk for lung cancer in never smokers in a GWAS and validated and replicated in two further cohorts. Study size: 754 (GWAS); 988 (validation); 530 (replication). Study population/ethnicity: Never smokers; USA. Significance metric(s): OR = 1.46 (95% CI 1.26-1.70; p = 5.94x10(-6). Type of association: CO.]
~0.80x reduced cancer risk
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rs763110, also known as -844C>T, is a SNP in the FAS ligand FASLG gene. A meta-analysis of 19 published studies, including 11,105 cancer cases and 11,372 controls, concluded that the rs763110(C;T) and (T;T) genotypes were associated with a significantly reduced (about 0.80x) cancer risk of all cancer types.
higher risk of Interstitial lung disease, and testicular cancer
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23andMe blog rs2736100 C 1.27 Glioma Lung cancer susceptibility locus at 5p15.33. Common genetic variants on 5p15.33 contribute to risk of lung adenocarcinoma in a Chinese population. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study. Role of 5p15.33 (TERT-CLPTM1L), 6p21.33 and 15q25.1 (CHRNA5-CHRNA3) variation and lung cancer risk in never-smokers. Individuals susceptible to lung adenocarcinoma defined by combined HLA-DQA1 and TERT genotypes. New insights into susceptibility to glioma. Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium. Evaluatio...
Magnitude: 2
Frequency: 22.1%
Repute:Good
References:61
Frequency: 22.1%
Repute:Good
References:61
decreased risk for colorectal cancer and lung cancer source
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miRNA sequences and non-small cell lung cancer rs11614913 SNP in hsa-mir-196a2 was associated with survival in individuals with NSCLC. Specifically, survival was significantly decreased in individuals who were homozygous CC at SNP rs11614913. microRNA 1,009 breast cancer cases and 1,093 controls in a population of Chinese women *rs11614913 in hsa-mir-196a2 T>C 1.23; 95% confidence interval [CI], 1.02-1.48 *rs3746444 in hsa-mir-499 A>G OR 1.25; 95% CI, 1.02-1.51 Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Signatures of purifying and local positive selection in human miRNAs. MicroRNA polymorphisms: the future of pharmacogenomics...
Significantly increased risk of developing lung cancer
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rs663048 associated with lung cancer The homozygotes for the variant allele had more than a 3-fold risk compared with the wild-type homozygotes [combined odds ratio (OR), 3.32; 95% confidence interval (95% CI), 1.81-7.21]. Heterozygotes also had a significantly elevated risk of lung cancer from the combined replication studies with an OR of 1.15 (95% CI, 1.04-1.59). The effect remained significant after adjusting for age, gender, and pack-years of tobacco smoke.007;67(17):8406-11].
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
1.33x increased risk of Ulcerative Colitis, but much lower Type 1 Diabetes risk. This raises the risk of Ulcerative Colitis (according to 23andMe), but also greatly lowers the risk of Type 1 Diabetes. It may also affect other autoimmune diseases.
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A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ancestry, concluded that this SNP and several others were associated with altered risk for the disease. [PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 6p21.32; Reported Gene(s): BTNL2, HLA-DRA, HLA-DRB5, HLA-DRB1, HLA-DQA1, HLA-DQB1; Risk Allele: rs2395185-?); (p-value= 0.0000000000000001).This variant is associated with Ulcerative colitis.] [OMIM:?] [GWAS:Ulcerative colitis]
2x higher risk for skin cancer; possibly other cancers
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rs25487 is a SNP also known as Gln399Arg, located in the DNA repair gene XRCC1. The (A) allele encodes the Gln amino acid. In one study of ~1000 Caucasians, the rs25487(A;A) genotype had significantly reduced risk of both basal cell [BCC; odds ratio 0.7, CI: 0.4-1.0] and squamous cell cancer (SCC; odds ratio 0.6, CI: 0.3-0.9). In a study of ~300 Koreans, rs25487(A;G) and (G;G) genotypes had an approximately 2-fold increased risk of basal cell cancer compared to rs25487(A;A) individuals (adjusted odds ratio 2.324, CI: 1.11-4.86, respectively). A small study (113 cases) of Hispanics with non-small cell lung cancer found an odds ratio of 1.52 per rs25487(A) allele (CI: 1.01-2.28). A study of 200 patients with Hodgkin disease compared to controls concluded that some risk was associated with th...
1.5x risk for ARMD
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rs3793784, a SNP upstream of the ERCC6 DNA repair gene, has been linked independently and in conjunction with another SNP (rs380390) to age related macular degeneration. On it's own, the odds ratios for increased risk for heterozygotes and homozygotes, were, respectively, 1.51 (CI 1.07-2.11) and 1.60 (CI 0.99-2.61). In dbSNP orientation, individuals who are CFH gene SNP genotype rs380390(C;C) and are also rs3793784(G;G) for this (ERCC6) SNP are calculated to be at 23 fold higher risk for developing age related macular degeneration compared to individuals who are homozygous for the more common alleles (among Caucasians) at both loci (ie who are rs380390(G;G) and rs3793784(C;C). Genetic markers and biomarkers for age-related macular degeneration. ERCC6/CSB gene polymorphisms and lung cancer ...
1.75-fold reduced risk of developing lung cancer The frequency of the minor allele A of '''rs31489''' was 32.49% in cancer patients versus 45.79% in disease-free subjects. Subjects carrying one copy of minor allele A are at 1.75-fold reduced risk of developing lung cancer.
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[GWAS:Lung adenocarcinoma]
~1.2x increased risk for several types of cancer
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rs401681 is a SNP in the CLPTM1-like CLPTM1 gene. The following studies span several types of cancer, and over 30,000 cases and 45,000 controls. deCODE press release reports rs401681 linked to basal cell carcinoma and many cancers for individuals with shorter telomeres, whereas those with long telomeres are at greater risk of melanoma. Neighboring rs2736098 also increases risk of cancer by affecting telomerase reverse transcriptase. The risk of these different cancers conferred by these two SNPs appears to be independent. 23andMe blog rs2736098 and rs401681 linked to many cancers, including susceptibility to pancreatic cancer However, a very large study (encompassing thousands of cases and controls) found no association between rs401681 and either (1) mean telomere length, or, (2) breast c...
Lower C-Reactive Protein levels. 1.2x increased risk overall for cancers. This causes a lower median hsCRP Level of 1.40 mg/L in women. Strangely this was associated with a higher overall cancer risk (in Finnish people).
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rs1892534 is a SNP that was originally associated with C-reactive protein levels, and given other findings that suggest C-reactive protein levels may be predictive of cancer risk, was thought to be linked to cancer risk. A large study pooling data from 3 Finnish studies totaling over 18,000 individuals concluded that while the rs1892534(A) allele was not likely to be causative (relative to cancer), it is associated with increased risk for cancer overall. The odds ratio for 1 or 2 such alleles was 1.05 (CI: 0.90 - 1.23) and 1.2 (CI: 1.01 - 1.42) overall. Two other CRP SNPs (rs1169300 and rs2464196) were specifically associated with increased lung cancer risk. CRP SNPs were not associated with colorectal, prostate or breast cancer risk. [PharmGKB:Curated GWAS Results: Loci Related to Metabo...
Magnitude: 1.09
Frequency: 36.3%
Repute:Bad
References:0
Frequency: 36.3%
Repute:Bad
References:0
very slightly increased risk for lung cancer
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A GWAS study found a (slight but significant) association between rs12050604 and risk for lung cancer, with an odds ratio of 1.09 (p = 3.6 × 10e-6).
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rs2066853 has been associated with increased risk for colorectal polyps depending on the amount of meat eaten or overall exposure to heterocyclic amines. lung cancer in a Chinese population heterozygous rs2158041 OR=1.53 for GA vs compared with the (G;G) and rs7811989 OR=1.48 for (G;A) compared with the GG genotype) *rs2066853 (p.Arg554Lys) and cumulative cigarette smoking and the Lys/Lys genotype conferred an increased risk of lung cancer in the heavy smokers OR=3.36 [PharmGKB:In-Depth Very common variant with controversial associations.]
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[PharmGKB:Non-Curated GWAS Results: Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1 (Initial Sample Size: 1,154 cases, 1,137 controls; Replication Sample Size: 2,724 cases, 3,694 controls; Risk Allele: rs7626795-G).] [GWAS:Lung cancer]
Frequency: 20.4%
References:3
References:3
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[GWAS:Lung cancer]
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rs8178085 and rs12334811 with approaching dose-dependent effect on lung cancer predisposition, subjects carrying two to four risk genotypes were associated with a 43% decreased lung cancer risk compared with subjects carrying zero to one risk genotypes (adjusted odds ratio, 0.53; 95% confidence interval, 0.35-0.80). Moreover, the decreased risk associated with the combined genotypes of rs8178085 and rs12334811 was slightly more pronounced in nonsmokers and in carriers with ataxia-telangiectasia mutated rs228591 variant allele or ataxia-telangiectasia and Rad3-related rs6782400 wild-type homozygous genotype.
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[GWAS:Lung cancer]
Frequency: 33.9%
References:1
References:1
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[GWAS:Lung cancer]
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rs2228001, also known as Lys939Gln, K939Q, and K940Q, is a SNP in the DNA nuclear excision repair gene xeroderma pigmentosum complementation group C XPC gene. The Lys (K) allele is encoded by the rs2228001(A) allele. A meta-analysis of 16 studies with 6797 cancer cases and 9018 controls concluded that rs2228001(C;C) homozygotes had an increased overall cancer risk (odds ratio of 1.16, CI: 1.05-1.28) compared with (A;A) homozygotes. This was primarily a risk for lung cancer. [PharmGKB:Curated Risk or phenotype-associated allele: Not specified. Phenotype: This SNP was associated with clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): p = 0.0045 (ANOVA); p = 0.052 (QMIS); p = 0.0004 (KW) Type of association...
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lung cancer *rs7249320 OR: 0.30; 95% CI: 0.16-0.55; P: 0.0001 *rs3745523 and smoky coal use (OR: 9.40; P(interaction) = 0.07) *rs7249320 and rs2739476 (OR: 10.77; P(interaction) = 0.003)
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Genome-wide significant association between a sequence variant at 15q15.2 and lung cancer risk. In this study, we sought to confirm 7 variants with suggestive association to lung cancer (P < 10(-5)) in a recently published meta-analysis. In a GWA dataset of 1,447 lung cancer cases and 36,256 controls in Iceland, 3 correlated variants on 15q15.2 (rs504417, rs11853991, and rs748404) showed a significant association with lung cancer, whereas '''rs4254535''' on 2p14, rs1530057 on 3p24.1, rs6438347 on 3q13.31, and rs1926203 on 10q23.31 did not. [GWAS:Lung cancer]
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Polymorphisms within the C-reactive protein (CRP) promoter region are associated with plasma CRP levels. Genetic variation is associated with C-reactive protein levels in the Third National Health and Nutrition Examination Survey. Common variants in the CRP gene in relation to longevity and cause-specific mortality in older adults: the Cardiovascular Health Study. C-reactive protein (CRP) gene polymorphisms, CRP levels, and risk of incident coronary heart disease in two nested case-control studies. Genetic determinants of basal C-reactive protein expression in Filipino systemic lupus erythematosus families. Fine-mapping the genetic basis of CRP regulation in African Americans: a Bayesian approach. C-reactive protein, interleukin-6, and prostate cancer risk in men aged 65 years and older. I...
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[PharmGKB:Non-Curated GWAS results: Lung cancer susceptibility locus at 5p15.33. (Initial Sample Size: 2,971 cases, 3,746 controls; Replication Sample Size: 2,899 cases, 5,573 controls); (Region: 5p15.33; Reported Gene(s): TERT, CLPTM1; Risk Allele: rs402710-C); (p-value= 0.000004).This variant is associated with Lung cancer.] [OMIM:LUNG CANCER SUSCEPTIBILITY 3; LNCR3] [GWAS:Lung cancer]
Frequency: 55.0%
References:1
References:1
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rs10508266 and rs3750861 near KLF6 shows significant association with Lung cancer risk.
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635 lung cancer cases with onset of disease below 51 years of age and 1,300 controls. major alleles associated with increased in risk of early-onset lung cancer modified by smoking. *rs1938901 (P = 0.0089) *rs193008 (P = 0.0108) *rs996999 (P = 0.0459). For rs996999, significance vanished after correction for multiple testing. odds ratio between 1.2 and 1.3 (95% confidence interval, 1.0-1.5)
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lung cancer rs8042374 P = 7.75 x 10(-12) [PharmGKB:Curated GWAS results: Common 5p15.33 and 6p21.33 variants influence lung cancer risk. (Initial Sample Size: 1,952 cases, 1,438 controls; Replication Sample Size: 7,579 cases, 8,236 controls); (Region: 15q25.1; Reported Gene(s): NR; Risk Allele: rs8042374-?); (p-value= 7.99999999999999E-12).This variant is associated with Lung cancer.] [OMIM:LUNG CANCER SUSCEPTIBILITY 2; LNCR2]
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[GWAS:Lung cancer]
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rs8178085 and rs12334811 with approaching dose-dependent effect on lung cancer predisposition, subjects carrying two to four risk genotypes were associated with a 43% decreased lung cancer risk compared with subjects carrying zero to one risk genotypes (adjusted odds ratio, 0.53; 95% confidence interval, 0.35-0.80). rs228591 variant allele or ataxia-telangiectasia and Rad3-related rs6782400 wild-type homozygous genotype
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lung cancer *rs7249320 OR: 0.30; 95% CI: 0.16-0.55; P: 0.0001 *rs3745523 and smoky coal use (OR: 9.40; P(interaction) = 0.07) *rs7249320 and rs2739476 (OR: 10.77; P(interaction) = 0.003)
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minor alleles for rs8034190, rs16969968 and rs1051730 significantly associated with lung cancer risk also in Japanese (odds ratio = 2.3)
normal
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rs1056836, also known as 4326C/G, Val432Leu or L432V, is a SNP in the cytochrome P450 1B1 (CYP1B1) gene. This gene is a member of the CYP1 gene family and one of the major enzymes involved in the hydroxylation of estrogens, a reaction likely to be relevant in hormonal carcinogenesis. [In dbSNP orientation, the (C) allele encodes the Leu; the (G) the Val.] In a study of 153 Hispanic Caucasians with prostate cancer the rs1056836(G;G) genotype showed decreased risk compared to the more common (C;C) genotype (odds ratio = 0.31, p = 0.04, CI: 0.10-0.96). This report cites another study as indicating that rs1056836(C;C) high-risk stage III and IV breast cancer patients receiving dose-intense paclitaxel in combination with doxorubicin and cyclophosphamide experience a longer progression-free surv...
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
normal
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rs2464196 is a SNP that was originally associated with C-reactive protein levels, and given other findings that suggest C-reactive protein levels may be predictive of cancer risk, was thought to be linked to cancer risk. A large study pooling data from 3 Finnish studies totaling over 18,000 individuals concluded that while this SNP is not likely to be causative (relative to cancer), it and one other CRP SNP (rs1169300) are associated with increased risk for lung cancer. The odds ratio for minor alleles of either SNP was about 1.5x and 2x for heterozygotes and homozygotes, respectively. One other CRP SNP (rs1892534) was associated with increased overall cancer risk. CRP SNPs were not associated with colorectal, prostate or breast cancer risk. [PharmGKB:Curated In a candidate gene-based ass...
normal
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rs1169300 is a SNP that was originally associated with C-reactive protein levels, and given other findings that suggest C-reactive protein levels may be predictive of cancer risk, was thought to be linked to cancer risk. A large study pooling data from 3 Finnish studies totaling over 18,000 individuals concluded that while this SNP is not likely to be causative (relative to cancer), it and one other CRP SNP (rs2464196) are associated with increased risk for lung cancer. The odds ratio for minor alleles of either SNP was about 1.5x and 2x for heterozygotes and homozygotes, respectively. One other CRP SNP (rs1892534) was associated with increased overall cancer risk. CRP SNPs were not associated with colorectal, prostate or breast cancer risk.
common in clinvar
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rs1800566 (C609T, Pro187Ser) is a snp within NQO1 (NAD(P)H dehydrogenase (quinone 1)). A Ser (T) at this location denotes the NQO1*2 allele. influences the risk of breast cancer according to the 23andMe blog rs1800566 increases susceptibility to Lung cancer 0.48 times for heterozygotes (CT) [PharmGKB:Curated Risk or phenotype-associated allele: C/T. Phenotype: There was no association between the NQO1*2 polymorphism and the risk of anthracycline-related CHF. Study size: 145. Study population/ethnicity: Nested case-control study was conducted within a cohort of 1979 patients enrolled in the Childhood Cancer Survivor Study who received treatment with anthracyclines and had available DNA. Significance metric(s): OR = 1.04; p = 0.97. Type of association: CO; TOX; ADR.] [OMIM:NAD(P)H DEHYDROGE...
normal
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rs2308327, also known as K178R, is a SNP in the MGMT gene. The more common allele, rs2308327(A), encodes a lysine (K) at codon 178, while the (G) allele encodes an arginine (R). In a pooled analysis of 200+ lung cancer patients, the rs2308327(G) allele was reported to provide a protective effect against lung cancer, and furthermore, more (G) alleles meant more protection, particularly for smokers. The odds ratios reported (p=0.003) were 0.67 (CI: 0.45-1.01) for heterozygotes, and 0.10 (CI: 0.01-0.94) for rs2308327(G;G) homozygotes. In a study of 300+ colon cancer cases, rs2308327(G), in linkage disequilibrium with the previously reported MGMT Ile(143)Val rs2308321 SNP, had an inverse association with colorectal cancer risk (odds ratio 0.52, CI: 0.35-0.78, unadjusted p(trend) = 0.0003 for t...
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rs3842 (A;G) and (G;G) was associated with increased risk of developing lung cancer (odds ratio [OR]. 1.36; 95% confidence interval [95% CI], 1.06-1.76), especially in women (2.5x) rs212090(A;T) (T;T) increased cancer susceptibility (OR, 1.37; 95% CI, 1.03-1.83)
common on affy axiom data
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lung cancer rs3117582 P = 4.97 x 10(-10) Update in lung cancer 2008. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Role of 5p15.33 (TERT-CLPTM1L), 6p21.33 and 15q25.1 (CHRNA5-CHRNA3) variation and lung cancer risk in never-smokers. [PharmGKB:Non-Curated Common 5p15.33 and 6p21.33 variants influence lung cancer risk. (Initial Sample Size: 1,952 cases, 1,438 controls; Replication Sample Size: 7,579 cases, 8,236 controls); (Region: 6p21.33; Reported Gene: BAT3MSH5; Risk Allele: rs3117582-C) This variant is associated with Lung cancer.] [OMIM:LUNG CANCER SUSCEPTIBILITY 4; LNCR4] [GWAS:Lung adenocarcinoma]
common in complete genomics
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rs10508266 and rs3750861 shows significant association with lung cancer risk rs3750861 affects expression of KLF6 splicing variants in prostate cancer and we found that its rare allele is associated with reduced lung cancer risk
common in complete genomics
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In this study, we sought to confirm 7 variants with suggestive association to lung cancer (P < 10(-5)) in a recently published meta-analysis. In a GWA dataset of 1,447 lung cancer cases and 36,256 controls in Iceland, 3 correlated variants on 15q15.2 (rs504417, rs11853991, and rs748404) showed a significant association with lung cancer, whereas rs4254535 on 2p14, '''rs1530057''' on 3p24.1, rs6438347 on 3q13.31, and rs1926203 on 10q23.31 did not. [GWAS:Lung cancer]
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
common in clinvar
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This SNP, a variant in the CHEK2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C). rs17879961 one of 3 SNPs associated with increased risk of lung cancer [OMIM:?] [GWAS:Lung cancer]
normal
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rs2279744, a variant in the promoter of the MDM2 gene and also known as '-410T-G', 'SNP309', and 'SNP309T>G', has been studied for several years to determine it's role in cancer origin and treatment. The interest primarily stems from the ability of the MDM2 protein to bind to and thereby enhance the degradation of the tumor suppressor protein known as p53. Studies on rs2279744 include: * rs2279744(G) carriers in individuals with cancer tend to develop such cancers on average 12 years earlier than those lacking this allele, and the frequency of rs2279744(G) was greatly increased in those who developed soft tissue sarcomas at a young age. * Individuals with one or more rs2279744(G) alleles who are also carriers of the TP53 rs1042522(C) (arg at aa72) SNP tend to develop cancers earlier tha...
common in complete genomics
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This SNP, a variant in the BRCA2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (T). [GWAS:Breast cancer]
51 snps
(hide) Lupus
Magnitude: 2
Frequency: 21.2%
Repute:Bad
References:29
Frequency: 21.2%
Repute:Bad
References:29
2x increased risk of developing SLE; 1.6x increased risk of developing primary biliary cirrhosis; and 1.7x increased risk of developing Sjögren's syndrome
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rs10488631, a SNP located 3' of the IRF5 gene, has been reported as a possibly causative SNP for systemic lupus erthymatosus (SLE), based on a study of ~700 Swedish patients. The risk allele is rs10488631(C), with a reported odds ratio of 2.07 (CI: 1.63-2.62, p = 9x10e-10). The C allele is also associated with primary biliary cirrhosis, with each C increasing the odds about 1.6 times. Each C allele increases risk of Sjögren's syndrome by 1.7 times. SLE rs10488631 and rs7582694 [OMIM:INTERFERON REGULATORY FACTOR 5; IRF5] [GWAS:Systemic lupus erythematosus]
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
HLA-DRB1*1501 carrier; higher multiple sclerosis risk Rs3135391(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.
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rs3135391 is highly correlated with the HLA-DRB1*1501 allele. The risk allele (T), is associated with a 3 to 6 fold higher risk for developing multiple sclerosis, and is the most significantly associated risk factor for MS. [PMC2892470] In one study, for example, the odds ratio was reported to be 3.04 (p < 1 x 10e-78). The HLA-DRB1*1501 allele has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and possibly narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. [PMC2892470] An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis would be to ensure...
1.4x increased risk for lupus
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rs17435 is one of several SNPs in the methyl CpG binding protein 2 (MECP2) that have been associated with risk for systemic lupus erythromatosis (SLE). The MECP2 gene is located on the X chromosome, which may be instructive since lupus is a predominantly female disease. An initial survey of 600 Korean patients, followed by 1,000 Caucasian patients, ultimately led to a meta-analysis indicating an odds ratio for the rs17435(T) risk allele of 1.39 (CI: 1.24–1.56, p = 1.2×10e-08). Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus. Replication of recently identified systemic lupus erythematosus genetic associations: a case-contro...
2.1x risk for Aspirin Induced Asthma. But possibly lower risk of intractible Grave's disease. Only tested in Japanese people. Might not be true for other races. May also be slightly protective against lupus (in Chinese people).
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rs4794067(C;C) and rs4794067(C;T) genotypes for the TBX21 gene are calculated to be at 2.15 fold higher risk (CI: 1.26-3.64) for aspirin-induced asthma (AIA) compared to rs4794067(T;T) homozygotes, based on a study of 72 patients vs 640 controls in a study of a Japanese population. Note that in this population, but perhaps not others, linkage disequilibrium exists between this SNP located upstream of the gene, rs4794067, and a common synonymous SNP located in the first exon, rs2074190, with a predictive accuracy of 92%. On the other hand, rs4794067(C;C) may greatly decrease the risk of lupus if rs17250932(C;C) is also present (at least in Chinese people). And those 2 SNPs also reduce the risk of intractable Graves' disease (at least in Japanese people).
3x higher risk of multiple sclerosis Rs3135388(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.
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rs3135388(T) is highly (> 99%) correlated with the HLA-DRB1*1501 allele; the risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. The risk per allele (or per haplotype) appears additive. It has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and, when linked with DQB1*0602, narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. Note: most publications refer to the risk allele as rs3135388(A), but in dbSNP and SNPedia orientation, it is rs3135388(T). An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis ...
complex; generally greater risk for cancer progression
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rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and H131R. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...
1.4x increased risk of SLE
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The rs2004640(A) allele had a higher frequency in SLE cases (0.385) than controls (0.321; odds ratio (OR) = 1.32, P = 0.0003). In combined analysis, including all seven independent cohorts from the three studies so far, robust and consistent associations of the rs2004640(A) allele with SLE were observed. The estimate of risk was OR = 1.44 (CI: 1.34-1.55), with an overall P = 1.85 x 10(-23) for the rs2004640(A) allele. The haplotype (rs2004640T-rs2280714A) involved in both the alternative splice donor site and the elevated expression of IRF5 also had a highly significant association with SLE (pooled, P = 2.11 x 10(-16)). Our results indicate that the genetic effect on the risk of SLE mediated by IRF5 variants can be generally accepted in both white and Asian populations. A meta-analysis com...
increased risk for auto-immune diseases
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The rs3087243 SNP is also known in the literature as the CT60 G>A or the +6230G>A polymorphism, and it is located in the CTLA4 gene. In Asian (Japanese) populations, the presence of an rs3087243(G) allele represents a 1.3 fold increased risk of autoimmune thyroid disease, and for those with autoimmune thyroid disease, a 1.5 fold increased risk of type-1 diabetes. However, in individuals without autoimmune thyroid disease, no association was seen between this SNP and type-1 diabetes. The authors speculate that earlier studies may have reported associations between this SNP and type-1 diabetes that were actually primarily based on the association with autoimmune thyroid disease. This same SNP, rs3087243, has also been implicated as a (minor) risk factor for developing rheumatoid arthri...
1.3x higher risk for endometrial cancer (in Chinese women)
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Category:interestingrs34330 shows an association with breast cancer in a British study involving ~2300 patients. The odds ratio for the (T;T) vs (C;C) homozygotes is 1.22 (CI: 1.02-1.47, p=0.013). found a significant association between rs34330 (-79C/T) and prostate cancer found higher odds for endometrial cancer among 1,200+ Chinese patients associated with rs34330, with an odds ratio of 1.33 (CI: 1.06-1.66) and 1.51 (CI: 1.16-1.94) for the (C;T) and (T;T) genotypes, respectively, compared with the (C;C) genotype. see also omim 176807 [OMIM:CYCLIN-DEPENDENT KINASE INHIBITOR 1B; CDKN1B] [GWAS:Systemic lupus erythematosus]
Magnitude: 1.2
Frequency: 39.8%
Repute:Bad
References:22
Frequency: 39.8%
Repute:Bad
References:22
slightly higher risk for lupus Slightly higher risk for lupus. This finding has been replicated across several populations, but in all, the effect is fairly small.
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rs17266594 rs10516487 rs3733197 gene associated with systemic lupus erythematosus. The association between rs10516487 and lupus was replicated in a study of 1892 European-derived SLE patients and 2652 European-derived controls; the odds ratio observed was 1.22 (CI: 1.11-1.34, corrected p-value=2.59 x 10e-5). [PharmGKB:Curated GWAS Results: Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus (Initial Sample Size: 279 cases, 515 controls; Replication Sample Size: 1,757 cases, 1,540 controls; Risk Allele: rs10516487-G).] [OMIM:B-CELL SCAFFOLD PROTEIN WITH ANKYRIN REPEATS 1; BANK1] [GWAS:Systemic lupus erythematosus]
Frequency: 10.6%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
Frequency: 11.5%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
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rs4728142, rs3807306 and a 5 bp insertion-deletion linked multiple sclerosis in three populations Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Exon expression in lymphoblastoid cell lines from subjects with schizophrenia before and after glucose deprivation. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus. Genetic risk factors in lupus nephritis and IgA nephropathy--no support of an overlap. Survival dimensionality reduction (SDR): development and clinical application of an innovative approach to detect epistasis in presence of right-cens...
1.4x increased risk for lupus
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rs1734787 is one of several SNPs in the methyl CpG binding protein 2 (MECP2) that have been associated with risk for systemic lupus erythromatosis (SLE). The MECP2 gene is located on the X chromosome, which may be instructive since lupus is a predominantly female disease. An initial survey of 600 Korean patients, followed by 1,000 Caucasian patients, ultimately led to a meta-analysis indicating an odds ratio for the rs1734787(C) risk allele of 1.42 (CI: 1.26–1.60, p = 1.6×10e-08).
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[GWAS:Systemic lupus erythematosus]
normal
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rs1734792 is one of several SNPs in the methyl CpG binding protein 2 (MECP2) that have been associated with risk for systemic lupus erythromatosis (SLE). The MECP2 gene is located on the X chromosome, which may be instructive since lupus is a predominantly female disease. An initial survey of 600 Korean patients, followed by 1,000 Caucasian patients, ultimately led to a meta-analysis indicating an odds ratio for the rs1734792(A) risk allele of 1.42 (CI: 1.24-1.58, p = 3.3E-08). Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus.
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[GWAS:Systemic lupus erythematosus]
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[GWAS:Alopecia areata]
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[GWAS:Systemic lupus erythematosus]
Frequency: 21.2%
References:3
References:3
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association with lupus risk allele is (G), odds ratio 1.95 (CI: 1.68-2.25, p = 2.710e-18) [GWAS:None]
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Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. [GWAS:Systemic lupus erythematosus]
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[OMIM:?] [GWAS:Systemic lupus erythematosus]
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T allele was significantly associated with the susceptibility to SLE (Z = 2.357, P = 0.018402) in dominant model
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rs4728142, rs3807306 and a 5 bp insertion-deletion linked multiple sclerosis in three populations Associated with systemic lupus erythematosus (SLE) in African Americans. [OMIM:INTERFERON REGULATORY FACTOR 5; IRF5] [GWAS:Rheumatoid arthritis]
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[GWAS:Systemic lupus erythematosus]
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[GWAS:None]
1.8x increased lupus risk
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rs1800630 is a SNP upstream of the tumor necrosis alpha (TNF) gene; this SNP is also typically called the -863 variant. In a study of 154 Thai patients with systemic lupus erythematosus (SLE), rs1800630(A) allele frequency was significantly increased, with an odds ratio of 1.85 (CI: 1.21-2.83, p(corr) = 0.009). This allele was also found to be significantly increased in the SLE group with Raynaud's phenomenon compared to SLE without Raynaud's phenomenon ( odds ratio of 2.23, CI: 1.21-4.10, p(corr) = 0.048). Separately, a meta-analysis of 10 case-control studies, including over 2,200 Graves' disease cases, concluded that rs1800630(A) carriers were associated with the disease.
Frequency: 31.0%
References:11
References:11
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An association was found between Systemic lupus erythematosus (SLE) and rs13192841. Three independent SNPs in the TNFAIP3 region (rs13192841, rs2230926 and rs6922466) are associated with systemic lupus erythematosus (SLE) among individuals of European ancestry. [OMIM:SYSTEMIC LUPUS ERYTHEMATOSUS, SUSCEPTIBILITY TO, 13; SLEB13] [GWAS:Multiple sclerosis]
Frequency: 33.0%
References:2
References:2
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[GWAS:Hippocampal atrophy]
Frequency: 34.5%
References:5
References:5
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[GWAS:Systemic lupus erythematosus]
Frequency: 35.4%
References:5
References:5
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Risk alleles for systemic lupus erythematosus in a large case-control collection and associations with clinical subphenotypes. Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. [OMIM:?] [GWAS:Systemic lupus erythematosus]
Frequency: 38.1%
References:25
References:25
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Associated with systemic lupus erythematosus (SLE) [PharmGKB:Non-Curated GWAS Results: Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX (Initial Sample Size: 1,311 cases, 3,340 controls; Replication Sample Size: 793 cases, 857 controls; Risk Allele: rs13277113-A).] [OMIM:FAMILY WITH SEQUENCE SIMILARITY 167, MEMBER A; FAM167A] [GWAS:Systemic lupus erythematosus] [GWAS:Systemic lupus erythematosus]
Frequency: 38.1%
References:10
References:10
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rs17266594 rs10516487 rs3733197 gene associated with systemic lupus erythematosus. The association between rs17266594 and lupus was replicated in a study of 1892 European-derived SLE patients and 2652 European-derived controls; the odds ratio observed was 1.22 (CI: 1.12-1.34, corrected p-value=1.97 x 10e-5). Study of functional variants of the BANK1 gene in rheumatoid arthritis. Replication of recently identified systemic lupus erythematosus genetic associations: a case-control study. Role of BANK1 gene polymorphisms in biopsy-proven giant cell arteritis. Identification of BANK1 polymorphisms by unlabelled probe high resolution melting: association with systemic lupus erythematosus susceptibility and autoantibody production in Han Chinese. [PharmGKB:Curated This variant is in strong linka...
Frequency: 38.9%
References:1
References:1
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association with lupus
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[GWAS:Systemic lupus erythematosus]
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[OMIM:?] [GWAS:Systemic lupus erythematosus]
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[GWAS:Systemic lupus erythematosus]
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[GWAS:Systemic lupus erythematosus]
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Although somewhat lacking in statistical power, several reports have linked rs1205, a UTR mutation known as CRP4 in the C-reactive protein CRP to the autoimmune disorder SLE, systemic lupus erythematosus. The risk allele in dbSNP orientation is (T). C-reactive protein (CRP) levels obesity rs1205(G) allele had significantly higher CRP levels than noncarriers in a dose-dependent manner suggesting a possible association with fat localization 23andMe blog each rs1205(T) lowered CRP by 20% but no association with heart disease. Analysis of polymorphisms in 16 genes in type 1 diabetes that have been associated with other immune-mediated diseases. A prospective assessment of the Y402H variant in complement factor H, genetic variants in C-reactive protein, and risk of age-related macular degenerat...
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[GWAS:Systemic lupus erythematosus]
Frequency: 44.2%
References:3
References:3
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[PharmGKB:Non-Curated GWAS results: Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus (Initial Sample Size: 431 cases, 2,155 controls; Replication Sample Size: 740 trios). This variant is associated with Systemic lupus erythematosus.] [GWAS:Systemic lupus erythematosus] [GWAS:Systemic lupus erythematosus]
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[GWAS:Systemic lupus erythematosus]
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[OMIM:?]
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[GWAS:Systemic lupus erythematosus]
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[GWAS:Systemic lupus erythematosus]
Frequency: 45.5%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
Normal risk of developing rheumatoid arthritis
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A variant located 64 bp upstream of the first untranslated exon (exon 1A), consisting of a 5 bp insertion/deletion CGGGG, may be the causative SNP in this region that is most responsible for increasing SLE risk, however it lacks an rs# (i.e. it isn't registered in dbSNP). A meta-analysis comprising 5 case-control studies, totaling 6,582 rheumatoid arthritis cases and 5,375 controls, concluded that several IRF5 gene SNPs were indeed (still) significantly associated with the disease. The rs729302(C) allele was associated with a slight protective effect (odds ratio 0.89, CI: 0.8-0.977, p = 0.015). [GWAS:Systemic lupus erythematosus]
Frequency: 46.9%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
Frequency: 46.9%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
Frequency: 46.9%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
Frequency: 47.8%
References:2
References:2
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rs12599402 is a SNP in the ch 16p13 region. A study totaling over 2,500 Han Chinese patients with systemic lupus erythematosus (SLE) concluded that rs12599402 was significantly associated with risk (p < 5 x 10e-8). The authors suspect that this SNP is tagging the same functional variant as previously reported in European populations. [GWAS:Systemic lupus erythematosus]
Frequency: 49.6%
References:5
References:5
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One of several SNPs found in a study of ~2,5720 female patients of European ancestry to be associated with systemic lupus erythematosus. [PharmGKB:Non-Curated GWAS results: Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci (Initial Sample Size: 720 cases, 2,337 controls; Replication Sample Size: 1,846 cases, 1,825 controls). This variant is associated with Systemic lupus erythematosus in women.] [GWAS:Systemic lupus erythematosus in women]
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rs231775, also known as +49A/G, is a SNP in the CTLA4 gene. which is linked to Hashimoto thyroiditis In a meta-analysis of CTLA4 gene SNPs, rs231775 was most associated with vitiligo; however, the association seems to hold only in the subgroup of patients with other autoimmune diseases. rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease associated with the development of placental abruption and preeclampsia, with women having the G allele being at risk rs231775 was not associated with type-1 diabetes in a study of 207 Portuguese patients. [PharmGKB:Curated This SNP affects risk for Autoimmune Thyroid Disorder (AITD). The G allele is generally thought to be the risk-conferring allele, but this study found that which allele confers ri...
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association with lupus A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Risk alleles for systemic lupus erythematosus in a large case-control collection and associations with clinical subphenotypes. Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
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[GWAS:Systemic lupus erythematosus]
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An association was found between systemic lupus erythematosus (SLE) and rs6922466. Three independent SNPs in the TNFAIP3 region (rs13192841, rs2230926, and rs6922466) are associated with systemic lupus erythematosus (SLE) among individuals of European ancestry. Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. Meta-analysis and imputation identifies a 109 kb risk haplotype spanning TNFAIP3 associated with lupus nephritis and hematologic manifestations. [OMIM:SYSTEMIC LUPUS ERYTHEMATOSUS, SUSCEPTIBILITY TO, 13; SLEB13]
Frequency: 55.0%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
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Evaluation of imputation-based association in and around the integrin-alpha-M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE). ITGAM is associated with disease susceptibility and renal nephritis of systemic lupus erythematosus in Hong Kong Chinese and Thai. Association of ITGAM polymorphism with systemic lupus erythematosus: a meta-analysis. [GWAS:Systemic lupus erythematosus]
Frequency: 59.3%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
Frequency: 59.3%
References:3
References:3
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[PharmGKB:Non-Curated GWAS results: Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus (Initial Sample Size: 431 cases, 2,155 controls; Replication Sample Size: 740 trios). This variant is associated with Systemic lupus erythematosus.] [GWAS:Systemic lupus erythematosus] [GWAS:Systemic lupus erythematosus]
1.9x increased risk for SLE (lupus)
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rs3748079 is a SNP in the promoter region of the ITPR3 gene; it is also known as -1990C>T. rs3748079 has been linked to increased risk for systemic lupus erythematosus (SLE) in two independent Japanese case-control samples (p=0.0000000178 with odds ratio of 1.88, CI:1.51-2.35). Individuals with risk genotypes of both rs3748079 and rs3095870, in the ITPR3 and NKX2.5 genes, respectively, have even high risk for SLE (odds ratio 5.77). This particular SNP also revealed associations with rheumatoid arthritis (RA) (p=0.0084 with odds ratio of 1.23, CI:1.05-1.43) and with Graves' disease (GD) (p=0.00036 with odds ratio of 1.57, CI:1.22-2.02). Note that the orientation of this SNP as published is reversed compared to the dbSNP entry. [OMIM:SYSTEMIC LUPUS ERYTHEMATOSUS; SLE]
normal risk of rheumatoid arthritis, SLE, Sjögren's syndrome, type-1 diabetes, and primary biliary cirrhosis.
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune dise...
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A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Risk alleles for systemic lupus erythematosus in a large case-control collection and associations with clinical subphenotypes. Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. [OMIM:?] [GWAS:Systemic lupus erythematosus]
1.1x increased risk for schizophrenia
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rs6932590 is a SNP that is postulated to have a role in conferring increased susceptibility for schizophrenia. rs6932590 lies in the major histocompatibility complex (MHC) region on chromosome 6, a region that codes for several genes with significant roles in autoimmunity, such as human leukocyte antigens. Specifically, rs6932590 lies in an intergenic region between PRSS16 (a serine protease expressed in the thymus that plays a role in positive T cell selection) and POM121L2 (a membrane glycoprotein) . The T allele at rs6932590 purportedly confers an increased risk for schizophrenia, with reported odds ratios of 1.16 and 1.31 . === Evidence === One large-scale case-controlled genome-wide association study (GWAS) that examined differential genotypes in individuals with schizophrenia, found ...
Frequency: 66.4%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
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[GWAS:Systemic lupus erythematosus]
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[GWAS:Systemic lupus erythematosus]
Frequency: 74.3%
References:9
References:9
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Associated with systemic lupus erythematosus (SLE) [PharmGKB:Non-Curated GWAS Results: Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX (Initial Sample Size: 1,311 cases, 3,340 controls; Replication Sample Size: 793 cases, 857 controls; Risk Allele: rs11574637-C).] [OMIM:INTEGRIN, ALPHA-X; ITGAX] [GWAS:Systemic lupus erythematosus]
Frequency: 76.1%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
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[GWAS:Systemic lupus erythematosus]
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[GWAS:Systemic lupus erythematosus]
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[GWAS:Systemic lupus erythematosus]
Frequency: 80.5%
References:3
References:3
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[PharmGKB:Non-Curated GWAS results: Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus (Initial Sample Size: 431 cases, 2,155 controls; Replication Sample Size: 740 trios). This variant is associated with Systemic lupus erythematosus.] [GWAS:Systemic lupus erythematosus] [GWAS:Systemic lupus erythematosus]
Frequency: 81.8%
References:3
References:3
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association with lupus [OMIM:?] [GWAS:Systemic lupus erythematosus and Systemic sclerosis]
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[GWAS:Systemic lupus erythematosus]
Frequency: 86.2%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
Frequency: 86.7%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
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[GWAS:Systemic lupus erythematosus]
Frequency: 88.3%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
Frequency: 93.8%
References:1
References:1
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[GWAS:Systemic lupus erythematosus]
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[GWAS:Systemic lupus erythematosus]
References:12
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Systemic Lupus Erythematosus rs10488631 rs2004640 rs10954213 and rs729302 Japanese 277 SLE patients and 201 controls. Carriers of the rs2004640T slightly increased among SLE patients (58.8%) as compared with controls (50.2%). When data from our Japanese population were combined with previously published data from a Korean population, the T allele frequency was found to be significantly increased in SLE patients (P = 8.3 x 10(-5)). While no association was observed for the rs10954213 . significant associations with 3 intron 1 SNPs (-4001, rs6953165, and rs41298401) were found. The allele frequency of rs41298401G was significantly decreased in SLE patients (13.0% versus 18.7% in controls; P = 0.017), and the allele frequency of rs6953165G, which was in absolute linkage disequilibrium with -4...
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[OMIM:INTERFERON REGULATORY FACTOR 5; IRF5]
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A polymorphism within IL21R confers risk for systemic lupus erythematosus with odds ratio 1.16
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rs762624(A;A) is associated with increased susceptibility to SLE and lupus nephritis
normal
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rs1734791 is one of several SNPs in the methyl CpG binding protein 2 (MECP2) that have been associated with risk for systemic lupus erythromatosis (SLE). The MECP2 gene is located on the X chromosome, which may be instructive since lupus is a predominantly female disease. An initial survey of 600 Korean patients, followed by 1,000 Caucasian patients, ultimately led to a meta-analysis indicating an odds ratio for the rs1734791(A) risk allele of 1.39 (CI: 1.24–1.57, p = 7.2×10-08). Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus. A common MECP2 haplotype associates with reduced cortical surface area in humans in two independ...
normal
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Several tightly linked SNPs in the STAT4 gene have been linked to risk for risk haplotype for systemic lupus erythematosus (SLE). The strongest association is found for either of two perfectly linked SNP alleles, rs10181656(G) and rs7582694(C), both yielding an odds ratio of 1.71 in this study of ~700 Swedish SLE patients. The risk for SLE was also calculated to increase as a function of the total number of risk alleles for this SNP plus 2 others in the IRF5 gene. Compared to individuals with 0 or 1 risk alleles, the risk for SLE increased 1.82-fold for each additional risk allele from this group. The odds ratio for SLE is 2.08 (CI: 1.53-2.83) for carriers of 2 risk alleles, and goes up to 13.0 (CI: 3.78-44.3) for carriers of 5 or 6 risk alleles (compared to those with 0 or 1). Association...
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
normal
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rs7528684 has been reported to be associated with rheumatoid arthritis in a Caucasian population, following reports of a similar association in a Japanese population. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 0.95 (CI 0.83-1.08), and for homozygotes, 2.30 (CI 1.64-3.23). In a study of 645 Caucasians from Southern Spain with multiple sclerosis, the rs7528684(G) allele (in dbSNP orientation) was found to be somewhat protective (per allele odds ratio 0.81, CI: 0.70-0.94, p=0.007). In another report , a summary indicates the following regarding disease and odds ratio (OR)for rs7528684: * for rheumatoid arthritis: OR = 2.15 (CI = 1.58–2.93), from 830 cases and 658 controls; * for SLE: OR = 1.49 (CI = 1.16â€...
normal
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CPMC uses this to indicate increased risk of Systemic lupus erythematosus. [GWAS:Systemic lupus erythematosus]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus (Initial Sample Size: 431 cases, 2,155 controls; Replication Sample Size: 740 trios). This variant is associated with Systemic lupus erythematosus.] [GWAS:Systemic lupus erythematosus] [GWAS:Systemic lupus erythematosus]
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
Magnitude: 0
Frequency: 81.5%
Repute:Good
References:2
Frequency: 81.5%
Repute:Good
References:2
normal
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This snp is in a gene which shows protein-protein interaction only with a mitochondrial protein. Mentioned in retracted [GWAS:Systemic lupus erythematosus]
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The T allele of rs9888739 is associated with higher risk of systemic lupus erythematosus. NEJM a combined analysis of the 7380 independent samples generated a maximum combined P=2.02x10–26 and an odds ratio of 1.65 for the association between the T allele of rs9888739 and lupus. [PharmGKB:Non-Curated GWAS Results: Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci (Initial Sample Size: 720 cases, 2,337 controls; Replication Sample Size: 1,846 cases, 1,825 controls; Risk Allele: rs9888739-T).] [GWAS:None] [GWAS:Systemic lupus erythematosus in women]
average
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In at least UK populations, and perhaps others, SNP rs2187668 is a tag SNP for the HLA-DRB1*0301 allele. The HLA-DRB1*0301 allele is the allele presenting the highest risk for developing lupus, and it appears to act in a dominant manner (i.e. inheriting 2 copies is no worse than inheriting 1 copy). In dbSNP orientation, the risk allele is rs2187668(A), with an odds ratio of 2.3x (CI: 1.7 - 3.2, permuted p < 0.0001). From individuals with the most common rs2187668(G;G) genotype, risk is reduced for celiac disease, with an odds ratio of 0.30x according to a study of ~800 patients. rs2187668(A) also tags the tightly linked DQB1*0201 allele, which in turn is linked to DQA1*0501; together, these are known as the DQ2.5 haplotype. This is the most common haplotype associated with celiac diseas...
Magnitude: 0
Frequency: 87.6%
Repute:Good
References:4
Frequency: 87.6%
Repute:Good
References:4
Magnitude: 0
Frequency: 91.2%
Repute:Good
References:1
Frequency: 91.2%
Repute:Good
References:1
Magnitude: 0
Frequency: 92.0%
Repute:Good
References:1
Frequency: 92.0%
Repute:Good
References:1
common in complete genomics
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Meta-analysis found 1.4x risk of rheumatoid arthritis for rs2230926(G;G) An association was found between Systemic lupus erythematosus (SLE) and rs2230926. Three independent SNPs in the TNFAIP3 region (rs13192841, rs2230926 and rs6922466) are associated with systemic lupus erythematosus (SLE) among individuals of European ancestry. Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. Meta-analysis and imputation identifies a 109 kb risk haplotype spanning TNFAIP3 associated with lupus nephritis and hematologic manifestations. Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23. Complex genetic association of 6q23 with autoimmune rh...
common in complete genomics
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functional haplotypes containing rs3091244/rs3093062 contain rs3093061 which is associated with SLE [OMIM:?]
normal
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Causal SNP in the ITGAM (CD11b) gene in patients with SLE who are of European or African descent;(P = 1.7 x 10(-17), odds ratio = 1.78). reconfirmed [PharmGKB:Curated This nonsynonymous SNP is an associated with risk of systemic lupus erythematosus in a study with 3,818 individuals of European descent.] [OMIM:INTEGRIN, ALPHA-M; ITGAM]
normal
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rs2279744, a variant in the promoter of the MDM2 gene and also known as '-410T-G', 'SNP309', and 'SNP309T>G', has been studied for several years to determine it's role in cancer origin and treatment. The interest primarily stems from the ability of the MDM2 protein to bind to and thereby enhance the degradation of the tumor suppressor protein known as p53. Studies on rs2279744 include: * rs2279744(G) carriers in individuals with cancer tend to develop such cancers on average 12 years earlier than those lacking this allele, and the frequency of rs2279744(G) was greatly increased in those who developed soft tissue sarcomas at a young age. * Individuals with one or more rs2279744(G) alleles who are also carriers of the TP53 rs1042522(C) (arg at aa72) SNP tend to develop cancers earlier tha...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 cause Aicardi-Goutieres syndrome at the AGS1 locus. Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 are associated with systemic lupus erythematosus. Clinical and molecular phenotype of Aicardi-Goutieres syndrome. [OMIM:?]
normal
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Although somewhat lacking in statistical power, several reports have linked rs1800947, a synonymous mutation known as CRP2 in the C-reactive protein CRP to the autoimmune disorder SLE, systemic lupus erythematosus. The risk allele in dbSNP orientation is (C). news C linked to lower CRP levels [OMIM:SYSTEMIC LUPUS ERYTHEMATOSUS; SLE]
common in complete genomics
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An association was found between Systemic lupus erythematosus (SLE) and rs5029939 (meta-analysis p = 2.89 x 10(-12), odds ratio 2.29). [PharmGKB:Curated GWAS results: Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus (Initial Sample Size: 431 cases, 2,155 controls; Replication Sample Size: 740 trios). This variant is associated with Systemic lupus erythematosus.] [OMIM:SYSTEMIC LUPUS ERYTHEMATOSUS, SUSCEPTIBILITY TO, 13; SLEB13] [GWAS:Systemic lupus erythematosus] [GWAS:Systemic lupus erythematosus]
111 snps
(hide) Lyme disease
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[PharmGKB:Curated The genotype distributions for the I602S variant in the TLR-1 gene differed significantly between patients with mild malaria and persons with asymptomatic infection. The 602S allele was associated with an odds ratio (OR) of 2.2 (P= .003) for malaria among patients with mild malaria.] [OMIM:TOLL-LIKE RECEPTOR 1; TLR1]
1 snp
(hide) Lymphoma
complex; generally greater risk for cancer progression
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rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and H131R. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...
0.42x reduced lymphoma risk
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Associated with (reduced) risk for follicular lymphoma. Based on studying ~1,300 patients in 2 populations, for (C;C) homozygotes, the odds ratio was 0.42 (CI: 0.23-0.77), and for the (C;T) heterozygotes, 0.64 (CI: .46-.88), p(trend) = 4x10e-4. estrogen receptor-positive breast cancer risk (C) have an Odds Ratio (OR) = 1.05 [95% Confidence Intervals (CI) 1.02-1.09] relative to t-allele homozygotes, P= 0.004. [PharmGKB:Curated In a French study population, the C allele of this SNP, which is located in intron 4 of ESR1, was associated with increased incidence of type 2 diabetes (diabetes mellitus, type 2). The C allele of this SNP was associated with increased fasting plasma glucose levels in Swedish males, although there was no significant association in the Swedish cohort between this SNP...
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rs7453920 adds an additional polymorphism to the growing body of literature supporting a genetic component to HBV infection and clearance. It is located in intron 1 of the HLA-DQB2 gene at the 6p21.32 locus. Therefore, the SNP does not affect the structure of the protein by any direct means. The A allele of this SNP has been associated with increased HLA-DQB2 mRNA levels in circulating monocytes (which are critical for mounting immune responses), increased HBV clearance, and CHB infection. Alleles 1 and 2 at this location are A and G with G being the risk allele (p = 5.98E-28; OR = 1.81). The HLA-DQB1 (Human Leukocyte Antigen) and HLA-DQB2 genes belongs to the HLA class II beta chain class paralogues. Class II molecules are heterodimers comprised of alpha (DQA) and beta (DQB) chains that a...
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[GWAS:Lymphoma]
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A US study of 1,172 lymphoma patients and 982 controls looked at 57 SNPs in 36 immune function genes. Five SNPs in two cytokine genes, tumor necrosis factor-alpha and lymphotoxin-alpha, were associated with a 1.31x increase in non-Hodgkin lymphoma (OR, 1.31; 95% CI, 1.06-1.63; P = 0.01) and with a 1.64x increase in the subtype known as diffuse large B cell lymphoma (OR, 1.64; 95% CI, 1.23-2.19; P = 0.0007). The other four SNPS are listed below. The cytokine genes affect inflammatory and innate immune responses. * rs1800629 * rs361525 * rs1799724 * rs2239704 [PharmGKB:Curated Risk or phenotype-associated allele, tested allele: unspecified; minor allele designation varies by ethnicity in dbSNP Phenotype: In 114 cases and 414 controls (n = 528), univariate analysis of disease association sho...
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A US study of 1,172 lymphoma patients and 982 controls looked at 57 SNPs in 36 immune function genes. Five SNPs in two cytokine genes, TNF and LTA, were associated with a 1.31x increase in Non-Hodgkin Lymphoma (OR, 1.31; 95% CI, 1.06-1.63; P = 0.01) and with a 1.64x increase in the subtype known as diffuse large B cell lymphoma (OR, 1.64; 95% CI, 1.23-2.19; P = 0.0007). The other four SNPS are listed below. The cytokine genes affect inflammatory and innate immune responses. * rs1800629 * rs361525 * rs1799724 * rs909253 [OMIM:LYMPHOTOXIN-ALPHA; LTA]
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[GWAS:Lymphoma]
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
normal risk
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rs1799724, a SNP near the tumor necrosis factor TNF gene, was found in a study of ~500 Caucasians to be both an independent risk factor for the development of Alzheimer's disease and also a modifier of the risk for individuals carrying ApoE4 alleles. On its own, the rs1799724(T) allele led to an odds ratio of 1.63 (CI: 1.13-2.34, p=0.009). In carriers of ApoE4 alleles, the odds ratio changed from 2.92 (CI: 2.00-4.27) in the absence of rs1799724(T) to an OR of 6.65 (CI: 3.26-13.55, p=0.03) in its presence. In a Chinese study , post-menopausal women were significantly more likely to have low bone mineral density if they had *CC-AA genotypes in rs1799724-rs1800629 * a haplotype of rs1799724-rs1800629-rs6254-rs6256-IL-1ra-rs2227956-rs1801197 news cigarette smoking and gastric cancer risk [Pha...
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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Macrophage activation syndrome in 13 children with systemic-onset juvenile idiopathic arthritis. [OMIM:?]
complex; generally normal risk
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rs361525 is also known as the TNF-238 SNP, and occasionally the rs361525(A) allele is referred to as 238.2 (with the more common (G) allele being 238.1). This SNP in the tumor necrosis factor-alpha gene has been linked to a wide variety of conditions: * Breast cancer ** A large study of over 5,000 Caucasian women found that rs361525(A) allele carriers were at somewhat elevated risk for breast cancer compared to the (G;G) genotype, with an odds ratio per allele of 1.18, CI: 1.04-1.35, p(trend)= 0.008. ** However, a 2009 European study of 30,000 breast cancer cases, compared to 30,000 controls, found no association, or as they put it, 'persuasive evidence against an overall association between invasive breast cancer risk and (this SNP)'. * Graft versus host disease (GVHD) ** A study of ~100 ...
12 snps
(hide) Lynch syndrome
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[OMIM:MSH2 POLYMORPHISM]
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Endometrial cancer risk is associated with variants of the mismatch repair genes MLH1 and MSH2. Partial loss of heterozygosity events at the mutated gene in tumors from MLH1/MSH2 large genomic rearrangement carriers. Association between DNA damage response and repair genes and risk of invasive serous ovarian cancer. Recurrent germline mutation in MSH2 arises frequently de novo. MLH1 -93G>A promoter polymorphism and the risk of microsatellite-unstable colorectal cancer. Implications of mismatch repair genes hMLH1 and hMSH2 in patients with sporadic renal cell carcinoma.
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colorectal cancer (-93G>A, rs1800734) 1,518 patients with CRC, homozygosity for the MLH1 -93A variant was associated with a significantly increased 3-fold risk of CRC negative for MLH1 protein by immunohistochemistry (odds ratio (OR): AA vs GG = 3.30, 95% CI 1.46-7.47, n = 1392, p = 0.004, MLH1 negative vs MLH1 positive CRC) and with a 68% excess of proximal CRC (OR: AA vs GG=1.68, 95% confidence interval (CI) 1.00-2.83, n = 1,518, p = 0.05, proximal vs distal CRC) [PharmGKB:Curated This promoter variant is a risk allele for the development of cancer after methylating chemotherapy for Hodgkin lymphoma.] [OMIM:MutL, E. COLI, HOMOLOG OF, 1; MLH1]
Frequency: 55.4%
References:1
References:1
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[Scientific basis for production of erythrocyte diagnosticums]. Mutational analysis of the PMS2 gene in sporadic endometrial cancers with microsatellite instability. Hereditary non-polyposis colorectal cancer and the role of hPMS2 and hEXO1 mutations. Screening for germline mutations of MLH1, MSH2, MSH6 and PMS2 genes in Slovenian colorectal cancer patients: implications for a population specific detection strategy of Lynch syndrome. Quantification of sequence exchange events between PMS2 and PMS2CL provides a basis for improved mutation scanning of Lynch syndrome patients. Clinical analysis of PMS2: mutation detection and avoidance of pseudogenes.
References:0
References:0
References:0
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs2020912 is a SNP in the MSH6 gene on chromosome 2, which (as a gene) has been associated with hereditary nonpolyposis colorectal cancer (HNPCC). It is not clear whether this variant predisposes individuals to cancers such as colorectal cancer. In ClinVar, some entries list it as pathogenic, most list it as benign, and one lists it as likely to be benign. Even so, this variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 600678.0006 [OMIM:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
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rs63749811 is a SNP in the MSH2 gene on chromosome 2, associated with Lynch syndrome (HNPCC). This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 609309.0008
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
(hide)
rs63749932 is a SNP in the MSH2 gene on chromosome 2, associated with Lynch syndrome (HNPCC). This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. Systematic analysis of hMSH2 and hMLH1 in young colon cancer patients and controls. Bethesda guidelines: relation to microsatellite instability and MLH1 promoter methylation in patients with colorectal cancer. Clinicopathological and molecular genetic analysis of 4 typical Chinese HNPCC families. Identification and survival of carriers of mutations in DNA mismatch-repair genes in colon cancer. Switching from tacrolimus to sirolimus halts the appearance of new sebaceous neoplasms in Muir-Torre syndrome.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
rs63750047 is a SNP in the MSH2 gene on chromosome 2, associated with Lynch syndrome (HNPCC). This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 609309.0006 [OMIM:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
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References:2
Repute:Good
References:2
common in clinvar
(hide)
rs63750217 is a SNP in the MLH1 gene on chromosome 3, associated with Lynch syndrome (HNPCC). This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 120436.0022 [OMIM:?]
Magnitude: 0
Repute:Good
References:0
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References:2
Repute:Good
References:2
common in clinvar
(hide)
rs63750451 is a SNP in the PMS2 gene on chromosome 7, associated with hereditary nonpolyposis colorectal cancer (HNPCC). This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 600259.0009 [OMIM:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
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Repute:Good
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Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
rs63750710 is a SNP in the MLH1 gene on chromosome 3, associated with Lynch syndrome (HNPCC). This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 120436.0008 [OMIM:?]
Magnitude: 0
Repute:Good
References:0
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Repute:Good
References:2
Repute:Good
References:2
common in clinvar
(hide)
rs63750899 is a SNP in the MLH1 gene on chromosome 3, associated with Lynch syndrome (HNPCC). This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 120436.0020 [OMIM:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
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Repute:Good
References:0
common in clinvar
(hide)
rs63750540 is a SNP in the MLH1 gene on chromosome 3, associated with Lynch syndrome (HNPCC). This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about.
common in clinvar
(hide)
rs63750875 is a SNP in the MSH2 gene on chromosome 2, associated with Lynch syndrome (HNPCC). The origin of this mutation appears to be in a population of Ashkenazi Jews. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 609309.0012 Characterization of chicken liver dihydrofolate reductase after purification by affinity chromatography and isoelectric focusing. Single-amplicon MSH2 A636P mutation testing in Ashkenazi Jewish patients with colorectal cancer: role in presurgical management. Homozygosity of MSH2 c.1906G-->C germline mutation is associated with childhood colon cancer, astrocytoma and signs of Neurofibromatosis type I. Classifyin...
common in clinvar
(hide)
rs63751207 is a SNP in the MSH2 gene on chromosome 2, associated with Lynch syndrome (HNPCC). This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 609309.0007 [OMIM:?]
198 snps
(hide) Malaria
complex; generally greater risk for cancer progression
(hide)
rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and H131R. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...
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[GWAS:Malaria]
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[GWAS:Malaria]
0.6x decreased risk for diabetic nephropathy in females with type-1 diabetes; increased malaria risk
(hide)
rs5498, also known as E469K or K469E, is a SNP in the ICAM1 gene that has been associated in some studies (and not others) with risk for type-1 diabetes (T1D). Studies involving Swedish and Japanese T1D patients have reported one or the other of the rs5498 alleles to represent increased T1D risk; studies involving British, Finnish, and Danish patients have not seen any association between rs5498 and T1D . In a study of the type-1 diabetes complication known as diabetic nephropathy (DN), 662 (312 female/350 male) T1D patients with DN and 620 (369/251) without DN were studied (all were Swedish Caucasians). The rs5498(G) allele was found to be significantly associated with decreased risk for diabetic nephropathy specifically in female T1D patients, with an odds ratio of 0.692 (CI: 0.5-0.958, ...
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rs1046089 is a SNP in the HLA-B associated transcript 2 BAT2 gene. A study of 2,162 case-controls found an association between rs1046089 and severe malaria. [GWAS:None]
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[GWAS:Malaria]
0.37x decreased risk for severe malaria
(hide)
rs1334512, also known as -53, is a SNP in the CD36 molecule (thrombospondin receptor) CD36 gene. A study of 552 individuals in India found a protective association between the rs1334512(T) allele and the (T;T) genotype related to severe malaria; (T;T) homozgyotes had a 0.37x (p = 0.004)decreased risk compared to (G;G) homozygotes.[http://7thspace.com/headlines/299292/variations_in_host_genes_encoding_adhesion_molecules_and_susceptibility_to_falciparum_malaria_in_india.html] Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples. Variations in host genes encoding adhesion molecules and susceptibility to falciparum malaria in India.
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ABO blood group rs8176719 represents a site in the ABO gene, and is a key SNP in determining blood group type O status. An allele that encodes either a blood group type A or type B will have a (G) at this SNP site, i.e. such an allele will be rs8176719(G). If a one-base deletion has occured at this site, removing this nucleotide all together, the corresponding allele is considered to be rs8176719(-) and encodes the most common blood group type O allele. However, an individual will typically only be blood group type O if they are carry two copies of (are homozygous) for this deletion, in other words, if their genotype is rs8176719(-;-). If they carry one copy, they could be blood type A, or blood type B (but are unlikely to be type O). A person who is rs8176719(G;G) is likely to be of blood...
References:4
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A study of 78 adult Thai patients infected with P. falciparum malaria reported that the TIM1 promoter haplotype comprising three derived alleles, -1637A rs7702919, -1549C rs41297577 and -1454A rs41297579, which were in complete linkage disequilibrium, was significantly associated with protection against cerebral malaria, a major life-threatening complication (OR = 0.41; CI: 0.24-0.71; P= 0.0009). [OMIM:HEPATITIS A VIRUS CELLULAR RECEPTOR 1; HAVCR1]
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[GWAS:Malaria]
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[OMIM:NATURAL CYTOTOXICITY TRIGGERING RECEPTOR 3; NCR3]
common on affy axiom data
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23andMe blog rs8177374(T) less susceptible to infection with malaria, tuberculosis, bacteremia and pneumococcal disease. [PharmGKB:Curated In a case-control study of 6,106 individuals from the UK, Vietnam and several African countries with invasive pneumococcal disease, bacteremia, malaria and tuberculosis the heterozygous carriage of this variant was associated independently with all four infectious diseases in the different study populations. Further this study found a protective effect of S180L heterozygosity against these infectious diseases. A second study could not confirm this association.] [OMIM:TIR DOMAIN-CONTAINING ADAPTOR PROTEIN; TIRAP]
common in clinvar The rs1050828 G allele is located within the G6PD gene and is associated with 'normal' levels of glucose-6-phosphate dehydrogenase enzyme production.
(hide)
rs1050828 is a SNP residing in the G6PD gene and is located the X chromosome. G6PD codes for the enzyme glucose-6-phosphate dehydrogenase, which helps protect the cell from oxidative damage. Depending on genotype, an individual may possess one of two primary versions of the G6PD gene; type A and type B. Type A is predominantly found in people who have African ancestry. Mutations of G6PD can cause varying degrees of G6PD deficiency, which is a disease affecting red blood cells. For example, an G to A substitution mutation at the rs1050828 (also referred to as G202A) is associated with a reduction of G6PD. The G6PD deficient genotype A- (~8-20% reduction of G6PD) is typically defined by the possession of the rs1050828 A allele (rs1050828(A;A)). In addition, individuals who are type A- almost...
common in complete genomics
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2020 African Americans. rs3211938, previously shown to influence malaria susceptibility, is documented to result in CD36 deficiency in a homozygous subject. This SNP conferred protection against the Metabolic Syndrome (p=0.0012, OR= 0.61, 95%CI: 0.46-0.82), increased high-density lipoprotein cholesterol, HDL-C (p=0.00018), and decreased triglycerides (p=0.0059) [OMIM:CD36 ANTIGEN; CD36]
G6PD Type B Resides within the glucose-6-phosphate dehydrogenase (G6PD) gene. The rs1050829 A allele is associated with G6PD 'type B', as well as, the production of 'normal' levels of G6PD enzyme.
(hide)
rs1050829 is a SNP within the G6PD gene and is located the X chromosome. G6PD codes for the enzyme glucose-6-phosphate dehydrogenase, which helps protect the cell from oxidative damage. Depending on genotype, an individual may possess one of two primary versions of the G6PD gene; type A and type B. Type A is predominantly found in people who have African ancestry. Mutations of G6PD can cause varying degrees of G6PD deficiency, which is a disease affecting red blood cells. For example, an A to G substitution mutation at the rs1050829 locus (also known as A376G) is associated with reduced production of G6PD enzyme. Other mutations causing G6PD deficiency include; rs1050828. The G6PD deficient genotype A- (~8-20% reduction of G6PD) is typically defined by the possession of both the rs1050829 ...
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asthma related This SNP is in the promoter region of the IL-13 gene PMID: 17615386 IL-13 is involved in pulmonary inflammation, remodeling and susceptibility to chronic obstructive pulmonary disease (COPD). This IL13 promoter polymorphism may modulate the adverse effects of cigarette smoking on pulmonary function in long-term cigarette smokers. Every 20 pack-year increment in smoking was associated with a 2.4% reduction in mean ppFEV1(forced expiratory volume in 1 second, a measure used to assess lung disease, like COPD) in the common homozygous (CC) or heterozygous (CT) promoter genotypes, and an 8.2% reduction in mean ppFEV1 in minor allele homozygotes (TT, recessive model). *pack-year= packs per day x years smoked rs1800925 and/or rs11568506 related to psoriasis and/or Crohn's disease ?...
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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rs33930165 is a relatively rare SNP found in the beta hemoglobin HBB gene, adjacent to the well-known SNP associated with malarial resistance (rs334). This SNP gives rise to the 'Hb C', or hemoglobin C, form of hemoglobin as the HBB forms are commonly named. It is found primarily in a subset of West Africa. rs33930165 is associated with increased malarial resistance, yet without giving rise to sickle cell anemia. A study of 4,000+ individuals in Burkina Faso found that rs33930165(A;G) heterozygotes had a 29% reduction in risk of clinical malaria (p = 0.0008), and rs33930165(C;C) homozygotes had a 93% reduction (p = 0.0011). [OMIM:?]
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
normal
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rs33950507 is a SNP found in the beta hemoglobin HBB gene, not far from the well-known SNP associated with malarial resistance (rs334, Hb S). This SNP gives rise to the 'Hb E', or hemoglobin E, form of hemoglobin as the HBB forms are commonly named. It is found primarily in Southeast Asia. rs33950507(A) is associated with somewhat increased malarial resistance, and in homozygous (A;A) state, with mild hypochromic microcytic anemia. Microarray-based estimation of SNP allele-frequency in pooled DNA using the Langmuir kinetic model. [OMIM:?]
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
21 snps
(hide) Male Infertility
Frequency: 23.4%
References:1
References:1
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each copy of a C at rs955988 (equivalent to rs12097821 in the study) was associated with 1.25 times higher odds of non-obstructive azoospermia
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each copy of a C at rs955988 (equivalent to rs12097821 in the study) was associated with 1.25 times higher odds of non-obstructive azoospermia
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SNP in the luteinizing hormone/chorionic gonadotropin receptor (LHCGR) gene, correlated to spermatogenetic damage and thus a risk factor for male infertility. Polymorphic variations in exon 10 of the luteinizing hormone receptor: functional consequences and associations with breast cancer. A luteinizing hormone receptor intronic variant is significantly associated with decreased risk of Alzheimer's disease in males carrying an apolipoprotein E epsilon4 allele. Genetic polymorphisms of GnRH and gonadotrophic hormone receptors affect the phenotype of polycystic ovary syndrome.
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each copy of a T at rs10910078 (equivalent to rs2477686 in the study) was associated with about 1.4 times higher odds of non-obstructive azoospermia .
Frequency: 44.2%
References:1
References:1
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each copy of a T at rs10910078 (equivalent to rs2477686 in the study) was associated with about 1.4 times higher odds of non-obstructive azoospermia .
Frequency: 53.1%
References:1
References:1
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[GWAS:Male infertility]
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rs3129878 is a SNP in the HLA gene region. It has been associated with slightly (~30%) higher risk for azoospermia (lack of sperm) and thus male infertility in both Chinese and Japanese men.
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[GWAS:Male infertility]
Frequency: 64.6%
References:1
References:1
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[GWAS:Male infertility]
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rs3129878 is a SNP on chromosome 6, within a gene known as chromosomal open reading frame 10 (C6orf10). It has been associated with slightly (~40%) higher risk for azoospermia (lack of sperm) and thus male infertility in Chinese but not Japanese men.
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rs10842262 associated with non-obstructive azoospermia
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
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Also known as c.102G>T transversion that results in an p.Arg34Ser amino acid. Low-frequency protamine 1 gene transversions c.102G->T and c.-107G->C do not correlate with male infertility Mutations in the protamine 1 gene associated with male infertility Male Infertility
13 snps
(hide) Malignant hyperthermia
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common
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rs121918593, aka p.Gly2434Arg or p.G2434R, is a SNP in the RYR1 gene leading to susceptibility to malignant hyperthermia when heterozygous. [OMIM:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common
(hide)
rs200563280, aka p.Arg2241X or p.R2241X, is a SNP in the RYR1 gene deemed highly pathogenic for malignant hyperthermia.
2 snps
(hide) Malignant melanoma
2-4x higher risk of sun sensitivity if part of risk haplotype. Increased risk of sunburns and freckles instead of tanning.
(hide)
rs1015362 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
2-4x higher risk of sun sensitivity if part of risk haplotype
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
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rs1006615 is associated with increased risk for schizophrenia in German and Scandinavian samples
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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The rs17878459(C) SNP defines the CYP2C19 allele known as CYP2C19*2B, or as E92D.
5 snps
(hide) Maple Syrup Urine Disease
Magnitude: 0
Frequency: 81.4%
Repute:Good
References:2
Frequency: 81.4%
Repute:Good
References:2
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Two SNPedia users have self reported the (T;T) genotype with no apparent consequences. It was first noted in a patient with documented in omim. A Japanese patient with the intermediate form of maple syrup urine disease 2 showed a compound heterozygote for both * the apparently causative C->G transversion at nucleotide 309 DBT gene (I37M) * this G->A transition in exon 9 (G323S) which with no obvious consequences [OMIM:?]
normal
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also known as rs79761867 (and formerly as rs28934895) but both share the (G;G) as normal plus strand orientation Maple Syrup Urine Disease, Type 1B
normal
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related to Maple Syrup Urine Disease Maple Syrup Urine Disease Type 1B rs386834233
3 snps
6 snps
(hide) Melanoma
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23andMe blog rs1393350 A 1.29 Melanoma rs1393350 increases susceptibility to Blond rather than brown hair 1.29 times for carriers of the A allele rs1393350 increases susceptibility to Blue rather than green eyes 1.52 times for carriers of the A allele rs1393350 increases susceptibility to Skin sensitivity to sun 1.26 times for carriers of the A allele A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Digital quantification of human eye color highlights genetic association of three new loci. [OMIM:TYROSINASE; TYR] [GWAS:Tanning]
~1.2x increased risk for several types of cancer
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rs401681 is a SNP in the CLPTM1-like CLPTM1 gene. The following studies span several types of cancer, and over 30,000 cases and 45,000 controls. deCODE press release reports rs401681 linked to basal cell carcinoma and many cancers for individuals with shorter telomeres, whereas those with long telomeres are at greater risk of melanoma. Neighboring rs2736098 also increases risk of cancer by affecting telomerase reverse transcriptase. The risk of these different cancers conferred by these two SNPs appears to be independent. 23andMe blog rs2736098 and rs401681 linked to many cancers, including susceptibility to pancreatic cancer However, a very large study (encompassing thousands of cases and controls) found no association between rs401681 and either (1) mean telomere length, or, (2) breast c...
1.12x increased risk for cutaneous melanoma
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rs13181 is a SNP of the XPD/ERCC2 gene. A meta-analysis of 20 studies, comprising 2,308 cases, ultimately concluded that the rs13181(G) allele is associated with increased cutaneous melanoma risk (odds ratio 1.12, CI: 1.03-1.21, p = 0.01; population attributable risk = 9.6%). Polymorphisms in XPD and TP53 and mutation in human lung cancer. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. ERCC1 and ERCC2 polymorphisms and adult glioma. [Correlation of genetic polymorphisms in nucleotide excision repair system to sensitivity of advanced non-small cell lung cancer patients to platinum-based chemotherapy]. Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes. Risk of non-Hodgk...
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eye color [GWAS:Eye color]
normal
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A study of 219 female melanoma patients and an equal number of controls concluded that 4 linked SNPs within the IL6R gene were associated with increased melanoma risk, but only when heterozygous. [Note that there may have been too few minor allele homozygotes to study, though.] The odds ratio associated with the minor allele of this SNP, rs6684439, was 1.74 (CI: 1.07-2.81). The 4 linked SNPs from identified in this study are: rs6684439, rs4845618, rs4845622, and rs8192284.
reduced risk of multiple myeloma
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A study of 219 female melanoma patients and an equal number of controls concluded that 4 linked SNPs within the IL6R gene were associated with increased melanoma risk, but only when heterozygous. The odds ratio associated with the minor allele of this SNP, rs8192284 (also known as Asp358Ala), was 1.68 (CI: 1.04-2.73). The 4 linked SNPs from identified in this study are: rs6684439, rs4845618, rs4845622, and rs8192284. linked to diabetes by multiple myeloma *rs1801278 [C/T versus C/C genotypes; OR, 4.3; 95% confidence interval (CI), 1.5-12.1] *rs6684439 (T/T versus C/C; OR, 2.9; 95% CI, 1.2-7.0) *rs7529229 (C/C versus T/T; OR, 2.5; 95% CI, 1.1-6.0) *rs8192284 (C/C versus A/A; OR, 2.5, 95% CI, 1.1-6.0) [OMIM:INTERLEUKIN 6 RECEPTOR; IL6R] [GWAS:Fibrinogen] [GWAS:C-reactive protein]
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23andMe blog rs2284063 A 1.20 Melanoma [OMIM:?] [GWAS:Melanoma]
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23andMe blog rs7023329 A 1.18 Melanoma [OMIM:TYROSINASE; TYR] [GWAS:Melanoma]
Magnitude: 1
Frequency: 73.5%
Repute:Good
References:1
Frequency: 73.5%
Repute:Good
References:1
Slightly lower risk of melanoma in individuals with low BMI Highly significant, replicated studies, p=3.6e-12. Risk allele A appears to represent a greater risk in those with low BMI, which is plausible due to the known role of FTO in obesity. This SNP is in intron 8, whereas BMI SNP's are usually in intron 1. The association was much stronger for those in the lowest quartile of BMI (1.66 per A allele risk) vs those in the other 3 quartiles (1.03 per A allele risk - no longer statistically significant). Risk for those in higher 3 quartiles of BMI is likely not substantially affected.
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[GWAS:Melanoma]
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This SNP occurs within CDK10, (cyclin-dependent kinase 10). The T variant has been associated with increased risk of Melanoma (OR=1.67, 95%CI 1.52-1.83) , (OR=2.26, 95%CI 1.32–3.88) . ==References== Genome-wide association study identifies three loci associated with melanoma risk. 23andMe blog rs258322 A (T in dbSNP): OR 1.67 for Melanoma [OMIM:TYROSINASE; TYR] [GWAS:Black vs. red hair color]
blue/gray eyes more possible
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rs1800407 is located in exon 13 of the OCA2 gene at amino acid position 419, and it is therefore also known as the R419Q variant. The (A) allele encodes the amino acid glutamine (instead of arginine), and it is associated with increased odds of having green/hazel eye color in some Caucasian populations. One copy of of rs1800407(A) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0012] According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour. Among rs12913832(A;A) individuals, the penetrance for green/hazel eye...
common
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rs4785763 is a SNP near the MC1R gene, which encodes the melanocortin 1 receptor. rs4785763 was found to be associated with melanoma based on a study by the eMERGE network in which electronic medical records were searched to find clinical associations associated with selected SNPs. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genome-wide association study of tanning phenotype in a population of European ancestry. [GWAS:Melanoma]
common in clinvar
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rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair color (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. blog about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0005 Melanoma [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]
normal
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A total of 2,019 cutaneous melanoma cases and 2,105 controls (Australians of European descent) were included in this genome-wide pooling association study. Using pooling, a new melanoma risk locus was identified on chromosome 20 (rs910873 and rs1885120; combined P < 1E-15. The per allele odds ratio was 1.75 (95% CI, 1.53-2.01), with evidence for stronger association in early-onset cases (age ≤40 OR, 1.83 (95% CI, 1.39-2.41); age >40 OR, 1.30 (95% CI, 1.00-1.69)). This study, which was conducted within the Nurses' Health Study, included 492 cases of non-melanoma skin cancer (NMSC; basal cell and squamous cell carcinomas) and 619 controls. The subjects were all Caucasian women, and the follow-up period was 28 years. rs910873, an ASIP gene-related SNP, was found to be associated w...
common in complete genomics
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One form of this SNP, known as N991D, A3199G or Asn991Asp for the nonsynonymous change it produces in the BRCA2 protein, has been reported to represent an increased risk for malignant melanoma. In a Polish study of ~600 patients in comparison with ~3700 controls, the rs1799944 SNP was found to have an odds ratio of 1.8. Patients with the homozygous rs1799944(G;G) genotype were present in 0.32% of malignant melanoma cases vs. 0.13% of controls. In two Chinese families with histories of inherited breast cancer, A1093C (Asn289His) in exon 10 and A3199G (Asn991Asp, i.e. rs1799944) in exon 11 of BRCA2 were found occurring together, and they were not seen in pooled control DNA. Risk of non-Hodgkin lymphoma (NHL) in relation to germline variation in DNA repair and related genes. DNA-repair geneti...
normal
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rs2279744, a variant in the promoter of the MDM2 gene and also known as '-410T-G', 'SNP309', and 'SNP309T>G', has been studied for several years to determine it's role in cancer origin and treatment. The interest primarily stems from the ability of the MDM2 protein to bind to and thereby enhance the degradation of the tumor suppressor protein known as p53. Studies on rs2279744 include: * rs2279744(G) carriers in individuals with cancer tend to develop such cancers on average 12 years earlier than those lacking this allele, and the frequency of rs2279744(G) was greatly increased in those who developed soft tissue sarcomas at a young age. * Individuals with one or more rs2279744(G) alleles who are also carriers of the TP53 rs1042522(C) (arg at aa72) SNP tend to develop cancers earlier tha...
16 snps
(hide) Menarche, age at
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Menarche
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Menarche
Frequency: 31.0%
References:0
References:0
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Menarche
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Menarche
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23andMe blog rs7861820(C) about five weeks earlier menarche. [OMIM:?] [GWAS:Menarche and menopause (age at onset)]
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23andMe blog rs314276 or the equivalent rs314263(T) yields *Female **menarche about six weeks earlier **1.2x accelerated breast development and a faster rate of increase in height and weight. **a reduction in adult height of about 0.15 inches. *Male **1.26 greater odds of advanced voice breaking at age 15 **1.19 times greater odds of advanced pubic hair at age 13 **faster rate of growth at age 10 and about a tenth of an inch less in adult height. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. [OMIM:?]
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23andMe blog rs314276 or the equivalent rs314263(T) yields *Female **menarche about six weeks earlier **1.2x accelerated breast development and a faster rate of increase in height and weight. **a reduction in adult height of about 0.15 inches. *Male **1.26 greater odds of advanced voice breaking at age 15 **1.19 times greater odds of advanced pubic hair at age 13 **faster rate of growth at age 10 and about a tenth of an inch less in adult height. [OMIM:?] [GWAS:Menarche (age at onset)]
Frequency: 46.9%
References:0
References:0
normal
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rs13357391 is a SNP in the - get ready - 'sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1' SPOCK1 gene. You gotta just love the names these fun-loving scientists come up with, don't ya? A study of 477 Caucasian women, followed up by replication studies in another ~1,600 and also 1,300+ Chinese women, found that several linked SNPs in the SPOCK1 gene are associated with age at menarche. rs13357391 replicated across all groups studied (p < 10e-3), with the minor (C) allele associated with a (slightly) earlier age at menarche.
normal
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rs1859345 is a SNP in the - get ready - 'sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1' SPOCK1 gene. A study of 477 Caucasian women, followed up by replication studies in another ~1,600 and also 1,300+ Chinese women, found that several linked SNPs in the SPOCK1 gene are associated with age at menarche. rs1859345 replicated across all groups studied (p < 10e-3), with the minor (C) allele associated with a (slightly) earlier age at menarche.
age at menarche ~2 months later on average
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rs2090409 is a SNP from chromosomal region 9q31.2 showing the strongest association with age at menarche in a study of 17,500 Icelandic women. Per copy carried of the rs2090409(A) allele, age at menarche is delayed about 1 month. [OMIM:?] [GWAS:Menarche]
10 snps
(hide) Meningioma
Magnitude: 1.4
Frequency: 39.8%
Repute:Bad
References:2
Frequency: 39.8%
Repute:Bad
References:2
1.4x increased risk for meningioma
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rs12770228 is a SNP in a region on ch 10p12.31 designated as the chromosome 10 open reading frame 114 C10orf114; it is just upstream of the MLLT10 gene. A study of ~1,600 patients with meningioma, all of European ancestry, concluded that increased risk for the disease was associated with rs12770228(A) alleles. The odds ratio was 1.37 (CI: 1.18-1.59, p = 4 x 10e-4). A nearby SNP, rs11012732, was also linked to meningioma risk.
Normal risk for meningioma
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rs4968451, which is in a breast cancer susceptibility gene, was associated with increased risk of meningioma, a common form of brain tumor, in a combination of five studies totaling 631 European patients. 'Meningioma risks associated with hetero- and homozygosity for the minor allele of were 1.61 (95% CI = 1.26 to 2.06) and 2.33 (95% CI = 1.25 to 4.34), respectively, and were thus compatible with a multiplicative model of action.' The risk allele and minor allele is rs4968451(C). Around 30% of Europeans carry one of risk genotypes, i.e. rs4968451(A;C) or (C;C); and perhaps 16% of meningiomas might be associated with this SNP.
2 snps
(hide) Mesothelioma
complex! see rs4880
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The rs4880(T) allele, part of the codon for amino acid valine at codon 16 of the antioxidant protein from the mitochrondrial superoxide dismutase 2 SOD2 gene, is the most common in most populations studied. The rs4880(C) allele gives rise to an alanine at this position is it also known as Val16Ala manganese superoxide dismutase, or A16V. There appears to be some conflict in the literature over the effect of this SNP. Having a valine at codon 16 is said to reduce enzyme activity , and thus lead to increased oxidative stress, yet in at least one study of the actual enzyme levels measured in people, SOD2 activity was 33% higher in (C;T) or (T;T) individuals compared to (C;C) individuals . Regardless of how this resolves, several phenotypic associations have been reported for this SNP, includi...
1 snp
(hide) Metabolic syndrome
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
normal
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
None
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Also known as I128T MTP rare allele of the MTP I128T polymorphism may be protective against impaired glucose tolerance, type-2 diabetes Association of polymorphisms in glutamate-cysteine ligase catalytic subunit and microsomal triglyceride transfer protein genes with nonalcoholic fatty liver disease. [OMIM:MICROSOMAL TRIGLYCERIDE TRANSFER PROTEIN, 88-KD; MTP]
4 snps
(hide) Migraines
some risk linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil).
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
1.1x higher risk for migraines
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rs2651899 is a SNP on ch 1p36.32 in the PRDM16 gene. A large GWAS study of over 5,000 patients with migraines and a meta-analysis concluded that this SNP was one of three influencing the condition, albeit with only slight risk increases on its own. The odds ratio for the slightly rarer rs2651899(G) allele was 1.11 (CI: 1.07 - 1.15, p = 3.8 x 10e-9). A 2013 study published by the American Headache Society reports significant influence of rs1835740, LRP1 rs11172113 and PRDM16 rs2651899 polymorphisms on migraine susceptibility in the Northern Indian population. Genome-wide-associated variants in migraine susceptibility: a replication study from North India. [GWAS:None]
2-6x increased risk for cluster headaches
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rs2653349, also known as G1246A, is a SNP in the HCRTR2 hypocretin-orexin gene. It has been linked primarily to cluster headaches. The more common allele (G) has been linked to increased risk; alternatively, this could be seen as implying that the less common (A) allele reduces cluster headache risk. In the (first) study, 100+ Italian patients were analyzed to reveal that rs2653349(G;G) genotypes were at 5x increased risk for the disorder, compared with (A;G) and (A;A) genotypes. A study of 200+ German patients indicated that (G;G) homozygotes were at 2x increased risk (CI: 1.32-2.92, p = 0.0007) for cluster headaches. A meta-analysis of 3 pooled studies concluded that the rs2653349(G;G) genotype showed a higher disease risk compared to the remaining genotypes (odds ratio 1.69, CI:1.11-2.5...
normal oral/throat cancer risk; more frequent alcohol consumption
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A SNP in rs1229984 encodes a form of the alcohol dehydrogenase ADH1B gene that significantly reduces the clearance rate of alcohol from the liver. This SNP is also known as Arg48His, with the (G) allele corresponding to the Arg and the (A) to the His. Known in the literature as ADH2*2 or sometimes ADH1B*2, the allele with increased activity (meaning more rapid oxidation of ethanol to acetaldehyde) is His48, encoded by rs1229984(A). Individuals with one or especially two ADH2*2 alleles, ie genotypes rs1229984(A;G) or rs1229984(A;A) are more likely to find drinking unpleasant and have a somewhat reduced risk for alcoholism. A study of over 3,800 cases of 'upper aerodigestive' cancers (mouth/throat, voice box, and esophageal cancers) concluded that the rs1229984(A) allele (in dbSNP orientatio...
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[GWAS:Migraine]
Frequency: 3.5%
References:1
References:1
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[GWAS:Migraine]
Frequency: 9.2%
References:1
References:1
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[GWAS:Migraine]
Frequency: 10.6%
References:1
References:1
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[GWAS:Migraine]
Frequency: 13.8%
References:1
References:1
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[GWAS:Migraine]
Frequency: 14.2%
References:1
References:1
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[GWAS:Migraine]
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[GWAS:None]
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[GWAS:Migraine]
Frequency: 17.7%
References:1
References:1
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[GWAS:Migraine]
Magnitude: 1
Frequency: 17.7%
Repute:Bad
References:1
Frequency: 17.7%
Repute:Bad
References:1
Migraine A four-marker haplotype in DDC was specific to migraine with Aura (rs2329340A, rs11974297C, rs2044859T, rs11761683G)
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a haplotype consisting of rs2329340(A), rs11974297(C), rs2044859(T) and rs11761683(G) associated with increased incidence of migraine with aura among a sample of 528 migraine patients (308 without aura, 220 with aura) and 528 sex-matched migraine-free controls
Frequency: 21.4%
References:1
References:1
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
Frequency: 24.8%
References:1
References:1
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[GWAS:Migraine]
Frequency: 28.3%
References:1
References:1
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[GWAS:Migraine]
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
Frequency: 33.8%
References:1
References:1
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[GWAS:Migraine]
Frequency: 37.5%
References:1
References:1
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[GWAS:Migraine]
Frequency: 38.9%
References:9
References:9
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rs11172113 is a SNP on ch 12q13.3 in the LRP1 gene. A large GWAS study of over 5,000 patients with migraines and a meta-analysis concluded that this SNP was one of three influencing the condition, albeit with only slight risk changes on its own. The odds ratio for the less common rs11172113(C) allele was 0.9 (CI: 0.87 - 0.93, p = 4.3 x 10e-9). [GWAS:None]
Frequency: 38.9%
References:1
References:1
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
normal
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
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a haplotype consisting of rs2329340(A), rs11974297(C), rs2044859(T) and rs11761683(G) associated with increased incidence of migraine with aura among a sample of 528 migraine patients (308 without aura, 220 with aura) and 528 sex-matched migraine-free controls Neurotransmitter systems and neurotrophic factors in autism: association study of 37 genes suggests involvement of DDC.
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[GWAS:Migraine]
Frequency: 44.2%
References:2
References:2
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a haplotype consisting of rs16827801(T) and rs10194776(G) associated with increased incidence of migraine without aura among a sample of 528 migraine patients (308 without aura, 220 with aura) and 528 sex-matched migraine-free controls
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[GWAS:Migraine]
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The T allele appears to be protective against high myopia. [GWAS:Migraine]
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[GWAS:Migraine]
Frequency: 46.2%
References:1
References:1
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
Frequency: 54.6%
References:1
References:1
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[GWAS:Migraine]
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[GWAS:Migraine]
Frequency: 57.9%
References:1
References:1
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
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a haplotype consisting of rs3027400(G) and rs2072743(C) associated with increased incidence of migraine without aura among a sample of 528 migraine patients (308 without aura, 220 with aura) and 528 sex-matched migraine-free controls
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[GWAS:Migraine]
Frequency: 65.5%
References:1
References:1
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[GWAS:Migraine]
Frequency: 65.8%
References:1
References:1
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[GWAS:Migraine]
Frequency: 67.7%
References:1
References:1
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[GWAS:Migraine]
Magnitude: 1
Frequency: 70.8%
Repute:Bad
References:2
Frequency: 70.8%
Repute:Bad
References:2
Major allele, normal risk of migraine
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rs10504861 is a SNP located on Chromosome 8q21 that was found to be associated with elevated incidence of migraine without aura in genome-wide association studies (GWAS). Migraine is a common but often incapacitating disease that affects up to 20% of the population, and affects 3-4 times as many women as men . Migraine can be classified into two main types: migraine with auras and migraines without auras. Migraine with auras accounts for a third of cases, where individuals experience a transient neurological symptom such as a visual, sensory, language or motor disturbance prior to an impending migraine attack . Migraines are thought to be caused by a mixture of genetic and environmental factors, with about two-thirds of patients reporting family history . rs10504861’s association with migr...
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
Frequency: 79.5%
References:1
References:1
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[GWAS:Migraine]
Frequency: 80.0%
References:1
References:1
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
Frequency: 87.6%
References:1
References:1
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[GWAS:Migraine]
Frequency: 89.2%
References:1
References:1
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
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[GWAS:Migraine]
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
normal
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rs1835740 is a SNP from the 8q22.1 chromosomal region, best known for harboring various genes involved in glutamate metabolism and transport. A large study comprising over 5,000 migraine patients and over 10,000 matched controls, primarily from Europe, found that the rs1835740(A) allele conferred a (slightly) higher risk for the disorder. The reported odds ratio was 1.18, (CI: 1.127–1.244, p = 1.69 × 10e-11).. However this study has failed to replicate in 2 followups.
normal risk
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Minor allele (T) of this SNP uniquely identifies what is known as the PROGINS allele in the progresterone receptor gene PGR. Two SNP's tagging a partial haplotype of the PGR gene were associated with an increased risk of ovarian cancer among homozygous carriers as compared with noncarriers: rs1042838 (PROGINS allele; odds ratio [OR] = 3.23, 95% confidence interval [CI] = 1.19 to 8.75, P = .022) and rs608995 (minor allele; OR = 3.10, 95% CI = 1.63 to 5.89, P<.001). The study suggest the effect is likely entirely due to rs608995, whose minor allele was almost always seen with PROGINS allele. For rs1042838, the risk allele in orientation to the corresponding dbSNP entry is (T). Subsequent studies have not replicated this high odds ratio, nor the apparent recessive model in this study. The ...
Magnitude: 0
Frequency: 67.6%
Repute:Good
References:6
Frequency: 67.6%
Repute:Good
References:6
common in complete genomics
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rs10166942 is a SNP on ch 2q37.1 in the TRPM8 gene. A large GWAS study of over 5,000 patients with migraines and a meta-analysis concluded that this SNP was one of three influencing the condition, albeit with only slight risk changes on its own. The odds ratio for the less common rs10166942(C) allele was 0.85 (CI: 0.82 - 0.89, p = 5.5 x 10e-12). [GWAS:None]
normal
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rs1800888, also known as Ile164, is a SNP in the beta 2 adrenergic receptor ADRB2 gene. The rs1800888(T) encodes the much rarer Ile allele. In a study of 330 patients undergoing percutaneous coronary intervention (PCI), patients carrying a rs1800888(T) allele showed a higher incidence of new acute myocardial infarction (17.5% vs. 4.5%, p = 0.001), new PCI (37.5% vs. 13.1%, p < 0.0001), and cardiac death (10% vs. 3.1%, p = 0.036). Regression analysis identified rs1800888(T) as an independent predictor of cardiac death (odds ratio 3.731, CI: 1.004 - 13.867, p = 0.049) and an overall major adverse cardiac event (odds ratio 4.1, CI: 1.945 - 8.640, p = 0.0001). A replication study was done on a population of 150 patients with peripheral artery disease. The presence of the rs1800888(T) allele...
common
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A study of ~100 German patients suffering from migraines reported SNP rs1043994 to be significantly associated with increased risk. Genetic variants of the NOTCH3 gene in the elderly and magnetic resonance imaging correlates of age-related cerebral small vessel disease. Two novel mutations and a previously unreported intronic polymorphism in the NOTCH3 gene.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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[Association of the polymorphisms of sodium transport related genes with essential hypertension]. [OMIM:MIGRAINE, FAMILIAL HEMIPLEGIC, 2]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs16022, also known as E918D, is a SNP in the calcium channel, voltage-dependent, P/Q type, alpha 1A subunit CACNA1A gene. On it's own it is not associated with migraines; however, individuals with both this SNP and a variant rs16023 have a 2x increased risk of any type of migraine, at least if a study of ~100 Italian patients is correct.
80 snps
(hide) Mucolipidosis type IV
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs104886461, also known as IVS3-2A>G or IVS3-2A-G, is a mutation in the mucolipin-1 MCOLN1 gene. This SNP represents the most common mutation in Ashkenazi Jews leading to Mucolipidosis type IV, an autosomal recessive neurodegenerative lysosomal storage disorder. Somewhere between 1 in 50 and 1 in 150 individuals of Ashkenazi Jewish ancestry are estimated to be (heterozygous) carriers for this SNP. Screening of Ashkenazi Jews for carriers of this SNP is recommended by the American College of Medical Genetics (ACMG; See also: OMIM [http://www.ncbi.nlm.nih.gov/omim/605248?db=omim&dopt=Detailed#605248Variants0001 605248.0001 [OMIM:?]
2 snps
(hide) Mucopolysaccharidosis
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Human beta-galactosidase gene mutations in morquio B disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Impaired elastic-fiber assembly by fibroblasts from patients with either Morquio B disease or infantile GM1-gangliosidosis is linked to deficiency in the 67-kD spliced variant of beta-galactosidase. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
common in clinvar
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rs72555391, also known as R482H or Arg482His, is a SNP in the galactosidase, beta 1 GLB1 gene. Two defective alleles in the GLB1 can lead to Mucopolysaccharidosis type IVB, and the rs72555391(A) allele is considered such a causative allele. However, clinical symptoms vary widely between individuals. [OMIM:?]
9 snps
(hide) Multiple myeloma
2.5x lower risk for multiple myeloma versus CC This SNP is in strong LD with rs1801278, rs6684439, and rs8192284 and likely to represent the same risk allele of the IL-6 receptor gene.
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multiple myeloma *rs1801278 [C/T versus C/C genotypes; OR, 4.3; 95% confidence interval (CI), 1.5-12.1] *rs6684439 (T/T versus C/C; OR, 2.9; 95% CI, 1.2-7.0) *rs7529229 (C/C versus T/T; OR, 2.5; 95% CI, 1.1-6.0) *rs8192284 (C/C versus A/A; OR, 2.5, 95% CI, 1.1-6.0)
Frequency: 39.8%
References:14
References:14
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[GWAS:Celiac disease]
reduced risk of multiple myeloma
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A study of 219 female melanoma patients and an equal number of controls concluded that 4 linked SNPs within the IL6R gene were associated with increased melanoma risk, but only when heterozygous. The odds ratio associated with the minor allele of this SNP, rs8192284 (also known as Asp358Ala), was 1.68 (CI: 1.04-2.73). The 4 linked SNPs from identified in this study are: rs6684439, rs4845618, rs4845622, and rs8192284. linked to diabetes by multiple myeloma *rs1801278 [C/T versus C/C genotypes; OR, 4.3; 95% confidence interval (CI), 1.5-12.1] *rs6684439 (T/T versus C/C; OR, 2.9; 95% CI, 1.2-7.0) *rs7529229 (C/C versus T/T; OR, 2.5; 95% CI, 1.1-6.0) *rs8192284 (C/C versus A/A; OR, 2.5, 95% CI, 1.1-6.0) [OMIM:INTERLEUKIN 6 RECEPTOR; IL6R] [GWAS:Fibrinogen] [GWAS:C-reactive protein]
Normal risk for development of MGUS This was defined as an OR of 1.0 for the development of MGUS (Monoclonal Gammopathy of Uncertain Significance). A is the major allele and not the risk allele.
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[GWAS:Hematological and biochemical traits]
common in clinvar
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[PharmGKB:Curated This variant may be associated with risk of developing glioma.] [OMIM:MULTIPLE MYELOMA, RESISTANCE TO]
normal
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The INSR A-603G promoter rs1864010 SNP, which is located within a known Sp1-binding site, was associated with the risk of colorectal cancer, with carriers of the G allele having a decreased risk (odds ratios (OR) 0.71, 95% confidence interval (CI) 0.54-0.93). Carrying the variant allele of the IRS1 Gly972Arg rs1801278 SNP further decreased the risk among the INSR-603G allele carriers (OR 0.28, 95% CI 0.11-0.70) multiple myeloma *rs1801278 [C/T versus C/C genotypes; OR, 4.3; 95% confidence interval (CI), 1.5-12.1] *rs6684439 (T/T versus C/C; OR, 2.9; 95% CI, 1.2-7.0) *rs7529229 (C/C versus T/T; OR, 2.5; 95% CI, 1.1-6.0) *rs8192284 (C/C versus A/A; OR, 2.5, 95% CI, 1.1-6.0)
7 snps
(hide) Multiple sclerosis
Increased risk of Multiple Sclerosis.
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rs3129934 is a SNP near the HLA-class II region that may be associated with several autoimmune diseases. In a study of two cohorts (Spanish and American multiple sclerosis patients, each numbering several hundred), rs3129934 was the SNP most associated with increased risk for multiple sclerosis. The odds ratio was 3.3 (CI: 2.3 - 4.9, p = 9 x 10e-11). Seven other SNPs were also identified in this study as associated with increased risk for MS. associated with type-1 diabetes. 1.6x risk of type-1 diabetes? 23andMe uses rs9273363 instead of rs3129934 in its reports on type 1 diabetes risk. This SNP was formerly used as a proxy for rs9272346, with this explanation: 'Note: the 2007 Wellcome Trust paper reported a strong association between type 1 diabetes and the SNP rs9272346. Our quality cont...
HLA-DRB1*1501 carrier; higher multiple sclerosis risk Rs3135391(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.
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rs3135391 is highly correlated with the HLA-DRB1*1501 allele. The risk allele (T), is associated with a 3 to 6 fold higher risk for developing multiple sclerosis, and is the most significantly associated risk factor for MS. [PMC2892470] In one study, for example, the odds ratio was reported to be 3.04 (p < 1 x 10e-78). The HLA-DRB1*1501 allele has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and possibly narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. [PMC2892470] An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis would be to ensure...
Magnitude: 2
Frequency: 52.2%
Repute:Bad
References:4
Frequency: 52.2%
Repute:Bad
References:4
>1.17x increased risk for multiple sclerosis
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rs10984447 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with this allele is 1.17 (CI 1.09-1.25). [PharmGKB:Curated GWAS Results: Risk alleles for multiple sclerosis identified by a genomewide study (Initial Sample Size: 931 trios, 2,431 controls; Replication Sample Size: 609 trios, 2,322 cases, 2,987 controls; Risk Allele: rs10984447-A).] [GWAS:Multiple sclerosis]
1.5x increased risk for multiple sclerosis
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The (C) allele of rs6897932, located in the alternatively spliced exon 6 of IL7RA gene and encoding the amino acid threonine rather than isoleucine at amino acid position 244, is associated with a slight increase (18%) in risk of developing multiple sclerosis. [PMID 17660817; Nature Genetics 39, 1083 - 1091 (2007) SG Gregory et al.] Note that the (C) allele is the most common at this position in all known populations and influences the ratios of the alternative isoforms (membrane bound and soluble) of the gene. blog post giving perspective on the significance of this snp a significant risk factor for multiple sclerosis in four independent (overall P = 2.9 x 10(-7)) influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silenc...
3x higher risk of multiple sclerosis Rs3135388(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.
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rs3135388(T) is highly (> 99%) correlated with the HLA-DRB1*1501 allele; the risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. The risk per allele (or per haplotype) appears additive. It has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and, when linked with DQB1*0602, narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. Note: most publications refer to the risk allele as rs3135388(A), but in dbSNP and SNPedia orientation, it is rs3135388(T). An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis ...
Slightly increased risk for multiple autoimmune diseases, such as type-1 diabetes Higher risk of type-1 diabetes.
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rs763361, also known as Gly307Ser, is a SNP in the immune response CD226 gene. The rs763361(T) allele (in dbSNP orientation) encodes the Ser. Based on multiple studies (by one group) now totaling over 2,000 patients, the rs763361(T) allele is associated with increased risk for multiple autoimmune diseases, including type-1 diabetes (p = 3 x 10e-9), multiple sclerosis (p = 4 x 10e-4), and possibly rheumatoid arthritis (p = 0.017). Based on tag SNP analysis, the authors conclude that this SNP could be the causal variant. Tested in a large multiple sclerosis data set consisting of 2369 trio families, 5737 cases and 10 296 unrelated controls, SNP rs763361 was associated with disease risk (p = 5.4 x 10e-8) [PharmGKB:Non-Curated GWAS Results: Robust associations of four new chromosome regions f...
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[GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
Frequency: 11.1%
References:1
References:1
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[GWAS:Multiple sclerosis]
Frequency: 11.5%
References:6
References:6
conflicting reports; possible slight increased risk for multiple sclerosis
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rs10492972 is a SNP in the KIF1B gene, which encodes a neuroprotein. A genome-wide association study of 2,679 patients with multiple sclerosis (and 3,000+ controls) concluded that the rs10492972(C) allele is a risk allele for the disease, with an odds ratio of 1.35 (p = 2.5 x 10e-10). This is one of the few SNPs associated with multiple sclerosis that is not related to immune function. A 2011 report combining eight data sets of cases and controls and three independent data sets of the International Multiple Sclerosis Genetic Consortium excluded the rs10492972(C) allele as a major 'risk' allele for MS with a high degree of confidence (p = 1.18 × 10e-4), i.e. they say it's not a risk allele. Genetic control of human brain transcript expression in Alzheimer disease. Meta-analysis of geno...
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rs4728142, rs3807306 and a 5 bp insertion-deletion linked multiple sclerosis in three populations Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Exon expression in lymphoblastoid cell lines from subjects with schizophrenia before and after glucose deprivation. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus. Genetic risk factors in lupus nephritis and IgA nephropathy--no support of an overlap. Survival dimensionality reduction (SDR): development and clinical application of an innovative approach to detect epistasis in presence of right-cens...
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The genetic aspects of multiple sclerosis. The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. Replication of top markers of a genome-wide association study in multiple sclerosis in Spain. [PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 978 cases, 883 controls; Replication Sample Size: NR); (Region: 13q31.3; Reported Gene(s): GPC5; Risk Allele: rs9523762-?); (p-value= 0.000001).This variant is associated with Multiple sclerosis.] [OMIM:?] [GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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23andMe blog multiple sclerosis rs2248359 CYP24A1 T 0.90 [GWAS:None]
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23andMe blog multiple sclerosis rs7595037 PLEK G 0.87 [GWAS:None]
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23andMe blog multiple sclerosis rs4902647 ZFP36L1 T 0.88 [GWAS:None]
Frequency: 20.4%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 794 cases, 883 controls; Replication Sample Size: NR); (Region: 4q13.2; Reported Gene(s): CENPC1; Risk Allele: rs10518025-?); (p-value= 0.000004).This variant is associated with Multiple sclerosis (severity).] [GWAS:Multiple sclerosis (severity)]
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rs4728142, rs3807306 and a 5 bp insertion-deletion linked multiple sclerosis in three populations Associated with systemic lupus erythematosus (SLE) in African Americans. [OMIM:INTERFERON REGULATORY FACTOR 5; IRF5] [GWAS:Rheumatoid arthritis]
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[GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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Mapping the genetic architecture of gene expression in human liver. Association of MHC SNP genotype with susceptibility to type 1 diabetes: a modified survival approach. A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Quantitative trait loci for CD4:CD8 lymphocyte ratio are associated with risk of type 1 diabetes and HIV-1 immune control. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. D...
Frequency: 31.0%
References:11
References:11
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An association was found between Systemic lupus erythematosus (SLE) and rs13192841. Three independent SNPs in the TNFAIP3 region (rs13192841, rs2230926 and rs6922466) are associated with systemic lupus erythematosus (SLE) among individuals of European ancestry. [OMIM:SYSTEMIC LUPUS ERYTHEMATOSUS, SUSCEPTIBILITY TO, 13; SLEB13] [GWAS:Multiple sclerosis]
Frequency: 31.0%
References:1
References:1
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23andMe blog multiple sclerosis rs17066096 IL22RA2 G 1.14 [GWAS:None]
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Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. Fine mapping the TAGAP risk locus in rheumatoid arthritis. [PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs1738074-A).] [OMIM:CEL...
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rs870849, a SNP in the LAG3 gene, has been associated with multiple sclerosis. Analysis of polymorphisms in 16 genes in type 1 diabetes that have been associated with other immune-mediated diseases. Genome bioinformatic analysis of nonsynonymous SNPs.
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Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
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23andMe blog multiple sclerosis C 1.15x [GWAS:None]
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[GWAS:Multiple sclerosis]
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Repeatedly associated in genome association studies with type-2 diabetes, type-1 diabetes, multiple sclerosis, and coronary artery disease, according to Risk alleles for multiple sclerosis identified by a genomewide study. An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. [GWAS:Hepatitis C induced liver cirrhosis]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 794 cases, 883 controls; Replication Sample Size: NR); (Region: 6p23; Reported Gene(s): JARID2; Risk Allele: rs6941421-?); (p-value= 0.000006).This variant is associated with Multiple sclerosis (severity).] [GWAS:Multiple sclerosis (severity)]
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SNP rs8702, located in the KLC1 gene, has been reported to have a protective effect against the occurrence of multiple sclerosis. Specifically, the odds of a rs8702(G;G) individual - as oriented to the dbSNP entry, not as published - are reported to be 0.21 (CI: 0.018 - 0.88). A study of ~800 Swedish patients with Alzheimer's disease did not find an association to rs8702 independently, however, rs8702 interacted with ApoE4 carrier status in AD (p=0.006). Variability in the kinesin light chain 1 gene may influence risk of age-related cataract. Gene-environmental effects behind leukoaraiosis: a silent genetic variant of the kinesin protein can be activated in a subject with poorly controlled long-lasting hypertension.
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[GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. [GWAS:Multiple sclerosis]
Frequency: 40.7%
References:2
References:2
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[GWAS:Age-related macular degeneration]
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[GWAS:Crohn's disease]
Frequency: 41.6%
References:1
References:1
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[GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
Frequency: 42.0%
References:4
References:4
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23andMe blog multiple sclerosis rs11154801 MYB A 1.09 [GWAS:None]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 978 cases, 883 controls; Replication Sample Size: NR); (Region: 2q14.2; Reported Gene(s): EN1; Risk Allele: rs651477-?); (p-value= 0.000007).This variant is associated with Multiple sclerosis.] [GWAS:Multiple sclerosis]
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Source nature multiple sclerosis rs9268428(C) + rs6457594(A) + rs7451962(C)
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[OMIM:?] [GWAS:Multiple sclerosis]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of electrocardiographic and heart rate variability traits: the Framingham Heart Study (Initial Sample Size: 548-1,175 individuals, depending on measure (Framingham); Replication Sample Size: NR). This variant is associated with Electrocardiographic traits.] [GWAS:Multiple sclerosis] [GWAS:Electrocardiographic traits]
Frequency: 45.1%
References:4
References:4
1.09x increased risk for multiple sclerosis
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rs12487066 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with this allele is 1.09 (CI 1.03-1.16). [PharmGKB:Curated In a replicated GWAS of U.K. and U.S. case/parent trios, this variant was shown to be associated with multiple sclerosis risk.]
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[GWAS:Multiple sclerosis]
1.14x risk
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rs6498169 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with this allele is 1.14 (CI 1.08-1.21). [PharmGKB:Curated GWAS Results: Risk alleles for multiple sclerosis identified by a genomewide study (Initial Sample Size: 931 trios, 2,431 controls; Replication Sample Size: 609 trios, 2,322 cases, 2,987 controls; Risk Allele: rs6498169-G).] [OMIM:?] [GWAS:Multiple sclerosis]
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(PLoS) assoc. w/ multiple sclerosis in a small sample of 229 Sardinians, risk allele A, (2.07 OR, 95% CI 1.4-3.1), p = 0.002
1.2x increased type-1 diabetes risk; 1.2x increased multiple sclerosis risk
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associated with type-1 diabetes In a separate study, Sardinians with either type-1 diabetes (1,037 patients) or multiple sclerosis (1,498 patients) plus matched controls were genotyped for rs725613. In this study, the rs725613(A) allele was positively associated not only with type-1 diabetes (odds ratio 1.15, p = 5.1 x 10e-3) but also with multiple sclerosis (odds ratio = 1.21, p = 6.7 x 10e-5). rs725613 was strongly associated with T1D in the Han Chinese population (P = 0.00007, odds ratio (OR) = 0.527, 95% confidence interval (CI) = 0.383-0.726) Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes. The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. [OMIM:C-TYPE LECTIN DOMAIN...
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[GWAS:Multiple sclerosis]
Frequency: 46.9%
Repute:Bad
References:28
Repute:Bad
References:28
1.6x risk of type-1 diabetes
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rs12708716 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.19 (CI 0.97-1.45), and for homozygotes, 1.55 (CI 1.27-1.89). In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 0.81 (CI 0.77-0.86). Tested in a large multiple sclerosis data set consisting of 2369 trio families, 5737 cases and 10 296 unrelated controls, SNP rs12708716 was associated with disease risk (p = 1.6 x 10e-16) [PharmGKB:Curated GWAS results: Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample...
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[GWAS:Multiple sclerosis]
normal
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rs7326018 is a SNP on chromosome 13. In a study of two cohorts (Spanish and American multiple sclerosis patients, each numbering several hundred), rs7326018 was one of eight SNPs associated with increased risk for multiple sclerosis. The odds ratio was 1.8 (CI: 1.1 - 2.9, p = 0.0228).
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[GWAS:Multiple sclerosis]
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[GWAS:Inflammatory bowel disease (early onset)]
Frequency: 47.8%
Repute:Bad
References:2
Repute:Bad
References:2
1.11x risk
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rs11164838 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with this allele is 1.12 (CI 1.05-1.18). [PharmGKB:Curated In a replicated GWAS of U.K. and U.S. case/parent trios, this variant was shown to be associated with multiple sclerosis risk.]
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[GWAS:Multiple sclerosis]
normal
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rs1327328 is a SNP on chromosome 13. In a study of two cohorts (Spanish and American multiple sclerosis patients, each numbering several hundred), rs1327328 was one of eight SNPs associated with increased risk for multiple sclerosis. The odds ratio was 1.7 (CI: 1.2 - 2.5, p = 0.0042).
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 978 cases, 883 controls; Replication Sample Size: NR); (Region: 4q35.1; Reported Gene(s): MGC45800; Risk Allele: rs7672826-?); (p-value= 0.000008).This variant is associated with Multiple sclerosis.] [GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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Replication of top markers of a genome-wide association study in multiple sclerosis in Spain. [PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 978 cases, 883 controls; Replication Sample Size: NR); (Region: 8p23.2; Reported Gene(s): CSMD1; Risk Allele: rs1529316-?); (p-value= 0.000002).This variant is associated with Multiple sclerosis.] [GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 978 cases, 883 controls; Replication Sample Size: NR); (Region: 3q24; Reported Gene(s): ZIC1; Risk Allele: rs1841770-?); (p-value= 0.000008).This variant is associated with Multiple sclerosis.] [GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
Frequency: 52.4%
References:5
References:5
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rs17445836 is a SNP in the region of the IRF8 gene. A large study (~5,000 patients) found an increased risk for multiple sclerosis associated with rs17445836; the odds ratio for the minor allele was reported as 0.80 (CI: 0.72-0.89, p=3.73x10(-9)). [OMIM:?] [GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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[GWAS:None]
Frequency: 53.8%
References:1
References:1
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DeCode reports that rs11117432 is associated with risk of multiple sclerosis. [GWAS:None]
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23andMe blog multiple sclerosis rs2546890 IL12B G 0.87 [GWAS:None]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 978 cases, 883 controls; Replication Sample Size: NR); (Region: 3q23; Reported Gene(s): SLC25A36; Risk Allele: rs908821-?); (p-value= 0.000003).This variant is associated with Multiple sclerosis.] [GWAS:Multiple sclerosis]
Frequency: 54.1%
References:4
References:4
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 794 cases, 883 controls; Replication Sample Size: NR); (Region: 3q25.32; Reported Gene(s): FLJ16641; Risk Allele: rs12638253-?); (p-value= 0.000002).This variant is associated with Multiple sclerosis (severity).] [GWAS:Multiple sclerosis (severity)]
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Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
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[OMIM:?] [GWAS:Multiple sclerosis]
Frequency: 56.6%
References:0
References:0
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Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
Frequency: 56.6%
References:1
References:1
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[GWAS:Multiple sclerosis]
Frequency: 57.8%
References:2
References:2
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[GWAS:Multiple sclerosis]
Frequency: 59.5%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 794 cases, 883 controls; Replication Sample Size: NR); (Region: 7p21.3; Reported Gene(s): C1GALT1; Risk Allele: rs10259085-?); (p-value= 0.000004).This variant is associated with Multiple sclerosis (severity).] [GWAS:Multiple sclerosis (severity)]
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[GWAS:Multiple sclerosis]
normal risk of rheumatoid arthritis, SLE, Sjögren's syndrome, type-1 diabetes, and primary biliary cirrhosis.
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune dise...
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23andMe blog multiple sclerosis rs1077667 TNFSF14 T 0.88 [GWAS:None]
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[GWAS:Multiple sclerosis]
Frequency: 62.8%
References:1
References:1
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[GWAS:Multiple sclerosis]
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Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
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[GWAS:Multiple sclerosis]
Frequency: 65.2%
References:4
References:4
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 794 cases, 883 controls; Replication Sample Size: NR); (Region: 7q31.2; Reported Gene(s): MET; Risk Allele: rs10243024-?); (p-value= 0.000006).This variant is associated with Multiple sclerosis (severity).] [GWAS:Multiple sclerosis (severity)]
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DeCode reports that the GG genotype of rs929230 is associated with 0.92x odds of developing multiple sclerosis.
Frequency: 68.1%
Repute:Bad
References:10
Repute:Bad
References:10
a slight increase in risk of developing multiple sclerosis
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The (G) allele of rs12722489, located in the first intron of the IL2RA gene, is associated with a slight increase (25%) in risk of developing multiple sclerosis. [PMID tbd; NEJM 357, 29 July 2007, DA Hafler et al.] Note that the (G) allele is the most common at this position in all known populations. blog post giving perspective on the significance of this snp plos rs12722489 and rs2104286 influence multiple sclerosis and type-1 diabetes Haplotypic analysis of Wellcome Trust Case Control Consortium data. IL2RA and IL7RA genes confer susceptibility for multiple sclerosis in two independent European populations. The complex genetics of multiple sclerosis: pitfalls and prospects. Refining genetic associations in multiple sclerosis. IL2RA genetic heterogeneity in multiple sclerosis and type 1 ...
Frequency: 69.0%
References:1
References:1
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[GWAS:Multiple sclerosis]
Frequency: 70.8%
References:3
References:3
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association with multiple sclerosis
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rs4613763 increases susceptibility to Crohn's disease 1.56 times for carriers of the C allele [OMIM:INFLAMMATORY BOWEL DISEASE 18; IBD18] [GWAS:Crohn's disease]
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[GWAS:None]
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multiple sclerosis protective rs2300747(G) [OMIM:?] [GWAS:Multiple sclerosis]
Frequency: 77.0%
Repute:Bad
References:11
Repute:Bad
References:11
>1.24x risk
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rs12044852 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with this allele is 1.24 (CI 1.12-1.37). [PharmGKB:Curated In a replicated GWAS of U.K. and U.S. case/parent trios, this variant was shown to be associated with multiple sclerosis risk.] [OMIM:?]
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[GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 794 cases, 883 controls; Replication Sample Size: NR); (Region: 4q28.3; Reported Gene(s): LOC132321; Risk Allele: rs1478091-?); (p-value= 0.000002).This variant is associated with Multiple sclerosis (severity).] [GWAS:Multiple sclerosis (severity)]
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[GWAS:Multiple sclerosis]
Frequency: 88.5%
References:1
References:1
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[GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
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rs1800693 is a SNP in the tumor necrosis factor receptor superfamily, member 1A TNFRSF1A gene. A large study (~5,000 patients) found two SNPs in the TNFRSF1A gene that each (independently) increase risk for multiple sclerosis, rs1800693 and rs4149584. This SNP, rs1800693, is more common but increases risk less; the odds ratio is reported as 1.2 (CI: 1.10-1.31, p=1.6x10(-11)). [OMIM:?] [GWAS:Multiple sclerosis]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 978 cases, 883 controls; Replication Sample Size: NR); (Region: 20p13; Reported Gene(s): C20orf46; Risk Allele: rs397020-?); (p-value= 0.0000008).This variant is associated with Multiple sclerosis.] [GWAS:Multiple sclerosis]
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rs987106 increases susceptibility to Multiple sclerosis 0.79 times for heterozygotes (AT) and 1.26 times for homozygotes (TT) Study of the association between the CAPSL-IL7R locus and type 1 diabetes. [PharmGKB:Curated In a nordic case-control group consisted of 1,820 individuals with multiple sclerosis and 2,634 healthy controls this SNP in intron 6 of the IL7R gene confirmed association with multiple sclerosis.]
common
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rs1321172 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with this allele is 1.08 (CI 1.02-1.14). [PharmGKB:Curated In a replicated GWAS of U.K. and U.S. case/parent trios, this variant was shown to be associated with multiple sclerosis risk.]
>1.11x risk
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rs10735781 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with this allele is 1.11 (CI 1.05-1.18). An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. [PharmGKB:Curated In a replicated GWAS of U.K. and U.S. case/parent trios, this variant was shown to be associated with multiple sclerosis risk.]
>1.11x risk
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rs6680578 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with this allele is 1.11 (CI 1.04-1.17). [PharmGKB:Curated In a replicated GWAS of U.K. and U.S. case/parent trios, this variant was shown to be associated with multiple sclerosis risk.]
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
normal
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rs4959039 is a SNP located within the Class I HLA-G region of chromosome 6. Independently of the influence of the (nearby) HLA-DRB1*1501 allele, the rs4959039(G) was shown to be associated with increased risk for multiple sclerosis in a study of ~2,300 patients.
common
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rs7536563 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with this allele is 1.12 (CI 1.06-1.18). [PharmGKB:Curated In a replicated GWAS of U.K. and U.S. case/parent trios, this variant was shown to be associated with multiple sclerosis risk.]
common
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rs4763655 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with this allele is 1.10 (CI 1.04-1.17). [PharmGKB:Curated In a replicated GWAS of U.K. and U.S. case/parent trios, this variant was shown to be associated with multiple sclerosis risk.]
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rs3118470 increases susceptibility to Type I Diabetes 1.28 times for carriers of the C allele Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1). Joint genetic susceptibility to type 1 diabetes and autoimmune thyroiditis: from epidemiology to mechanisms. Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes. Genetic association between the interleukin-2 receptor-alpha gene and mode of onset of type 1 diabetes in the Japanese population. Overview of the Rapid Response data. Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families. [GWAS:Alopecia areata]
common
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rs6604026 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with this allele is 1.15 (CI 1.08-1.22). [PharmGKB:Curated GWAS Results: Risk alleles for multiple sclerosis identified by a genomewide study (Initial Sample Size: 931 trios, 2,431 controls; Replication Sample Size: 609 trios, 2,322 cases, 2,987 controls; Risk Allele: rs6604026-C).] [GWAS:Multiple sclerosis] [GWAS:Multiple sclerosis]
No increased risk. Not reported to be associated with an increased risk of multiple sclerosis. See The SH2D2A gene and susceptibility to multiple sclerosis. The T cell regulator gene SH2D2A contributes to the genetic susceptibility of multiple sclerosis rs926103 and a GA repeat polymorphism forming a risk haplotype for Multiple sclerosis
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Rs926103 is located within the SH2D2A gene on Chromosome 1. SH2D2A encodes an adapter protein thought to function in T-cell signal transduction. A study in the Journal for Neuroimmunology reported that 16 repeats repeat of GA after the (A;A) allele at this SNP is associated with multiple sclerosis in Norwegian, Danish and Swedish sample sets. The study concludes that the SH2D2A gene may contribute to susceptibility to MS. This study has yet to be verified or reproduced in any subsequent research. The T cell regulator gene SH2D2A contributes to the genetic susceptibility of multiple sclerosis rs926103 and a GA repeat polymorphism forming a risk haplotype for Multiple sclerosis The fact that this is a mixture of a snp and a repeat makes this an interesting test case for Promethease
normal
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rs7528684 has been reported to be associated with rheumatoid arthritis in a Caucasian population, following reports of a similar association in a Japanese population. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 0.95 (CI 0.83-1.08), and for homozygotes, 2.30 (CI 1.64-3.23). In a study of 645 Caucasians from Southern Spain with multiple sclerosis, the rs7528684(G) allele (in dbSNP orientation) was found to be somewhat protective (per allele odds ratio 0.81, CI: 0.70-0.94, p=0.007). In another report , a summary indicates the following regarding disease and odds ratio (OR)for rs7528684: * for rheumatoid arthritis: OR = 2.15 (CI = 1.58–2.93), from 830 cases and 658 controls; * for SLE: OR = 1.49 (CI = 1.16â€...
1.7x risk for RA; 1.6X for T1D; also MS?
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rs2104286 has also been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.30 (CI 1.02-1.65), and for homozygotes, 1.57 (CI 1.25-1.99). The same (A) allele of rs2104286, which is located in the first intron of the IL2RA gene, was calculated to confer a slight increase (19%) in the risk of developing multiple sclerosis. [PMID tbd; NEJM 357, 29 July 2007, DA Hafler et al.] Note that the (A) allele is the most common at this position in all known populations. blog post giving perspective on the significance of this SNP with respect to multiple sclerosis news announcement rs2104286 was significantly associated with UK cases of juvenile idiopathic arthritis (JIA)(allelic odds ra...
Magnitude: 0
Frequency: 69.0%
References:2
Frequency: 69.0%
References:2
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This SNP is located in the gene KANK1. This variant has been associated with risk of Multiple Sclerosis . The study analyzed 931 family trios and several different control sets. The p-value for the association was 9.945e-06 http://www.gwascentral.org/marker/HGVM3682090/results. [PharmGKB:Curated In a replicated GWAS of U.K. and U.S. case/parent trios, this variant was shown to be associated with multiple sclerosis risk.]
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
common in complete genomics
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23andMe blog multiple sclerosis rs9282641 CD86 A 0.83 [GWAS:None]
common in complete genomics
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Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
Magnitude: 0
Frequency: 81.4%
Repute:Good
References:1
Frequency: 81.4%
Repute:Good
References:1
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[GWAS:Multiple sclerosis]
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[GWAS:Multiple sclerosis]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (Initial Sample Size: 794 cases, 883 controls; Replication Sample Size: NR); (Region: 19p13.2; Reported Gene(s): ACP5; Risk Allele: rs7253363-?); (p-value= 0.000009).This variant is associated with Multiple sclerosis (severity).] [GWAS:Multiple sclerosis (severity)]
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[GWAS:Multiple sclerosis]
common
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rs7577363 has been reported in a large study to be associated with multiple sclerosis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with this allele is 1.37 (CI 1.17-1.61). [PharmGKB:Curated In a replicated GWAS of U.K. and U.S. case/parent trios, this variant was shown to be associated with multiple sclerosis risk.]
common on affy axiom data
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rs17824933 is a SNP in the region of the CD6 gene. A large study (~5,000 patients) found an increased risk for multiple sclerosis associated with rs17824933; the odds ratio for the minor allele was reported as 1.18 (CI: 1.07-1.30, p=3.79x10(-9)). [OMIM:?] [GWAS:Multiple sclerosis]
129 snps
(hide) Muscular dystrophy
Magnitude: 0
Frequency: 98.1%
Repute:Good
References:1
Frequency: 98.1%
Repute:Good
References:1
common in clinvar
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[OMIM:MUSCULAR DYSTROPHY, CONGENITAL, 1C, WITH NEUROLOGIC ABNORMALITIES]
common in clinvar
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omim notes that links this snp to Duchenne muscular dystrophy, but hapmap frequency makes that seem very unlikely. [OMIM:DUCHENNE MUSCULAR DYSTROPHY]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Caveolin-3 in muscular dystrophy. Mutations in the caveolin-3 gene: When are they pathogenic? Molecular and muscle pathology in a series of caveolinopathy patients. CAV3 gene mutation analysis in patients with idiopathic hyper-CK-emia. Caveolin-3 in muscular dystrophy. Mutations in the caveolin-3 gene: When are they pathogenic? CAV3 gene mutation analysis in patients with idiopathic hyper-CK-emia. Mutant caveolin-3 induces persistent late sodium current and is associated with long-QT syndrome. [OMIM:?]
11 snps
(hide) Myasthenia gravis
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[GWAS:Myasthenia gravis]
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[GWAS:Myasthenia gravis]
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[GWAS:Myasthenia gravis]
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[GWAS:Myasthenia gravis]
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
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[GWAS:Hematology traits]
normal
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rs4553808, also known as A/G-1661, is a SNP in the upstream activator sequence of the cytotoxic T lymphocyte associated antigen-4 CTLA4 gene. This gene encodes the CD152 antigen. A study of 165 Swedish myasthenia gravis patients concluded that the rs4553808(G;G) homozygotes had an odds ratio of 0.05 (CI: 0.00286-0.874, p=0.0023) for the disease compared to healthy individuals, while the rs4553808(G) allele showed a less dramatic reduction in risk, with an odds ratio of 0.578 (CI: 0.373-0.897, p=0.015).
7 snps
(hide) Myelofibrosis
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23andMe blog At rs12340895(G) (equivalent to rs12343867 in the study) had nearly four times higher odds of developing V617F-positive myelofibrosis (MPN) compared to people without the disease. 23andMe recently replicated this association, though we see a smaller effect — in our database, people with a G at rs12340895 have about two times the odds of developing V617F-positive MPN compared to people without the disease. n A at rs3780374 in the JAK2 gene (equivalent to rs4495487 reported in the study and highly correlated with rs12343867) have about three times higher odds of developing V617F-positive MPN compared to individuals without the A version. The following SNPs are (all) associated with the JAK2 46/1 haplotype that appears to predispose to V617F-positive neoplasms; since they a...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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rs77375493, also known as V617F or Val617Phe, is a variant considered to generally be acquired (i.e. somatic) in the Janus kinase 2 JAK2 gene. The wild-type (normal) allele is rs77375493(G), and the (very rare) variant allele is rs77375493(T). While the predictive medical consequences of having the variant in the absence of symptoms remain uncertain, this variant has been reported to be associated with several myeloproliferative disorders (basically, cancers of the blood), including polycythemia vera, essential thrombocythemia, and idiopathic myelofibrosis, and it appears to be act in a dominant manner. See: OMIM 147796.0001. A participant in the PGP, John Lauerman, has published an article about his experiences upon finding out that he carried this variant. [OMIM:?]
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23andMe blog At rs12340895(G) (equivalent to rs12343867 in the study) had nearly four times higher odds of developing V617F-positive myelofibrosis (MPN) compared to people without the disease. '23andMe recently replicated this association, though we see a smaller effect — in our database, people with a G at rs12340895 have about two times the odds of developing V617F-positive MPN compared to people without the disease. People with an A at rs3780374 in the JAK2 gene (equivalent to rs4495487 reported in the study and highly correlated with rs12343867) have about three times higher odds of developing V617F-positive MPN compared to individuals without the A version.' The following SNPs are (all) associated with the JAK2 46/1 haplotype that appears to predispose to V617F-positive neoplasm...
3 snps
(hide) Myocardial infarction
increased risk for celiac disease increased resistance to bacterial infections
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rs3184504 is a nonsynonymous SNP in the SH2B3 gene, and it is also known as R262W. In a recent (2008) study of non-HLA SNP associations of 1600+ celiac disease patients, this SNP was considered one of the most significant. The odds ratio for the minor allele was 1.19 (CI:1.10-1.30, p=1.33x10e-7). rs653178, another SNP in strong linkage disequilibrium (r<sup>2</sup>>0.99) with rs3184504, was also associated with celiac disease. associated with type-1 diabetes 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 23andMe blog blood pressure Pharmacogenetic implications for eight common blood pressure-associated...
1.2x risk of coronary artery disease
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rs599839 and rs4970834 explain about 1% of the variation in circulating LDL-cholesterol levels. 'When we look at this particular genetic variance, of all the cholesterol variation among the population, 1% of it can be attributed to this particular locus,' said Sandhu. 'This is equivalent to more established genes for LDL regulation, particularly APOE.' rs646776 also linked. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins found each minor allele to increase statin effectiveness by 1.3% (rs646776, β=−0.013, s.e.=0.002, P=1.05 × 10−9 and rs12740374, β=−0.013, s.e.=0.002, P=1.05 × 10−9). 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs1746...
No benefit to alcohol consumption
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rs708272, also known as the TaqIB polymorphism of the CETP gene, may influence the levels of the 'good' cholesterols, the high density lipoprotein (HDL) cholesterols. Generally, the B2 allele is considered to lead to higher HDL levels. However, high HDL cholesterol, at least when combined with another HDL raising SNP (rs1800588), doesn't appear to actually protect individuals from coronary artery disease, at least based on one study of ~800 Caucasian male patients. A similarly confusing picture emerges from a study of two populations of 10,000+ individuals each. The distribution of the CETP genotype was observed to be different in population-based studies compared with studies in populations selected by high cardiovascular risk, and contradictory results were seen when trying to figure out...
Myocardial Infarction Risk
This genoset looks for the genotypes which most strongly contribute to the risk of myocardial infarction according to http://www3.interscience.wiley.com/cgi-bin/fulltext/123217456/HTMLSTART These are *rs10116277 *rs599839 *rs1746048 *rs17465637 *rs9818870 *rs12526453 *rs3184504 *rs9982601 *rs6725887
MI risk, aspirin resistance 23andMe blog lower odds of early stent thrombosis
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The 'A2' allele of the platelet specific alloantigen system is encoded by rs5918(C), and it has been implicated as increasing the risk of myocardial infarctions, heart disease, and resistance to blood-thinning benefits of aspirin. On its own, the A2 allele is implicated especially in early onset heart disease ; in combination with the 4G allele of the PAI1 gene, rs1799889, the increased risk of myocardial infarction in a Finnish study population was 4 fold higher (odds ratio = 4.5, p=0.001), particularly in males (odds ratio = 6.4, p=0.0005) . Olympic skater Sergei Grinkov, who had this risk factor, died of a heart attack at age 28. A2 allele carriers also appear to be relatively resistant to the anti-thrombotic (i.e. anti-clotting) actions normally associated with aspirin] use. A protecti...
Magnitude: 2
Frequency: 50.0%
Repute:Bad
References:77
Frequency: 50.0%
Repute:Bad
References:77
1.3x risk for Heart Attack. Normal risk for Abdominal Aortic Aneurysm and Brain Aneurysm. One copy of an SNP that increases risk of Myocardial Infarction (Heart Attack) and other Coronary Heart Disease. It has been shown that regularly eating raw vegetables and fruit can reduce the risk to the same level as people without this SNP. This SNP also has the normal medium risk of abdominal aortic aneurysm (weakened artery to abdomen and legs) or brain aneurysm (weakened artery to brain).
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This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...
Magnitude: 1.34
Frequency: 50.0%
Repute:Bad
References:18
Frequency: 50.0%
Repute:Bad
References:18
1.34x higher risk for myocardial infarction
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rs17465637 is a SNP found to be associated with heart disease by the German MI (Myocardial infarction) Family Study group This 2011 study concluded that the only MIA3 gene SNP to be associated with increased risk for myocardial infarction is rs17465637, with an odds ratio of 1.17 (CI: 1.04-1.32) and 1.37 (CI: 1.08-1.74) for carriers of one or two (C) alleles, respectively. 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 con...
Some studies - but not others - report a slightly increased risk for myocardial infarction
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rs4977574 increases susceptibility to Coronary artery disease 1.30 times for heterozygotes (A;G) and 1.54 times for homozygotes (G;G) rs4977574 was found to be associated with myocardial infarction based on a study by the eMERGE network in which electronic medical records were searched to find clinical associations associated with selected SNPs. . In this study of 2,000 patients, rs4977574(G;G) homozygotes had an increased risk (odds ratio) for myocardial infarction of 1.84 (CI: 1.14−3.09, p = 0.011) [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 controls; Replication Sample Size: 9,746 cases, 9,746 controls); (Region: 9p21.3; Reported...
very slightly higher risk for myocardial infarction
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rs2291834 is a SNP in the MIA3 gene. Several studies, most notably perhaps by deCode scientists, have shown a (very slightly) elevated risk for myocardial infarctions to be associated with the rs2291834(C) allele.
1.48x risk
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rs1048990, also known as the exon-1 -8C/G SNP in the PSMA6 gene, has been reported in a large study of Japanese patients to be associated with increased risk for myocardial infarction (heart disease). The risk allele (oriented to the dbSNP entry) is (G). The odds ratio (based on an additive model) is 1.48 (CI 1.23-1.77, p = 1.2 x 10e-5). given the rarity of this variant in Caucasians, the attributable risk of rs1048990 for MI is unlikely to be great in western populations Various ways of calculating the association between rs1048990 and myocardial infarction all led to odds ratios of around 1.2 - 1.5 in a case-control association study on a cohort of 1,884 MI patients and 2,643 unrelated controls from the Chinese population. [OMIM:PROTEASOME SUBUNIT, ALPHA-TYPE, 6; PSMA6]
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Despite earlier reports of an association, no risk for myocardial infarction was seen for rs2660899 variants in a study of 1,211 German patients.
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23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 Coronary Heart Disease [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 controls; Replication Sample Size: 9,746 cases, 9,746 controls); (Region: 10q11.21; Reported Gene(s): CXCL12; Risk Allele: rs1746048-C); (p-value= 0.000000007).This variant is associated with Myocardial infarction (early onset).] [GWAS:Myocardial infarction (early onset)]
Normal risk of myocardial infarction
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rs1063192 is a SNP in the cyclin-dependent kinase inhibitor 2B CDKN2B gene. A study of 432 Han Chinese patients with myocardial infarctions concluded that male subjects carrying a rs1063192(C) allele were at 0.71x decreased risk (for MI). Myocardial Infarction [GWAS:Vertical cup-disc ratio]
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667 cases and 862 controls (OR=0.87, P=0.046, 95% CI=0.72-0.99 for rs135551; OR=0.80, P=0.034, 95% myocardial infarction in a European population.
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Coronary Heart Disease [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 controls; Replication Sample Size: 9,746 cases, 9,746 controls); (Region: 19p13.2; Reported Gene(s): LDLR; Risk Allele: rs1122608-G); (p-value= 0.000000002).This variant is associated with Myocardial infarction (early onset).] [GWAS:Coronary artery disease]
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A US study of 1,172 lymphoma patients and 982 controls looked at 57 SNPs in 36 immune function genes. Five SNPs in two cytokine genes, tumor necrosis factor-alpha and lymphotoxin-alpha, were associated with a 1.31x increase in non-Hodgkin lymphoma (OR, 1.31; 95% CI, 1.06-1.63; P = 0.01) and with a 1.64x increase in the subtype known as diffuse large B cell lymphoma (OR, 1.64; 95% CI, 1.23-2.19; P = 0.0007). The other four SNPS are listed below. The cytokine genes affect inflammatory and innate immune responses. * rs1800629 * rs361525 * rs1799724 * rs2239704 [PharmGKB:Curated Risk or phenotype-associated allele, tested allele: unspecified; minor allele designation varies by ethnicity in dbSNP Phenotype: In 114 cases and 414 controls (n = 528), univariate analysis of disease association sho...
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rs20455, often called Arg719 or 719Arg, is a reasonably well studied SNP in the KIF6 gene. The risk allele (encoding the arginine at position 719) is rs20455(C). An extensive 2010 meta-analysis, including over 17,000 patients, suggests this variant does not significantly influence coronary artery disease risk. This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 pos...
normal
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827 males and 709 females, 606 subjects without cancer and 930 subjects with various cancers *rs1041981(A;C) (C804A, T60N) associated with lung cancer (CA + AA: CC, adjusted OR = 0.60, 95% CI = 0.37 - 0.97), in males but not in females [OMIM:MYOCARDIAL INFARCTION, SUSCEPTIBILITY TO]
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rs9551963, also known as SG13S32, is an ALOX5AP gene SNP that has been defined as part of a haplotype potentially associated with risk for myocardial infarction or ischemic stroke. Details of this haplotype and several related studies are on the ALOX5AP page. Genetic effects in the leukotriene biosynthesis pathway and association with atherosclerosis. 5-Lipoxygenase activating protein (ALOX5AP) gene variants associate with the presence of xanthomas in familial hypercholesterolemia. Oxidative risk for atherothrombotic cardiovascular disease. The role of LTA4H and ALOX5AP genes in the risk for asthma in Latinos. ALOX5AP and LTA4H polymorphisms modify augmentation of bronchodilator responsiveness by leukotriene modifiers in Latinos.
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association with myocardial infarction
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[GWAS:Myocardial infarction]
1.75x risk of MI
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This SNP, located on chromosome 2 in a gene (VAMP8) associated with platelet activation, may be associated with early onset myocardial infarction (MI). The risk allele for this SNP (in dbSNP orientation) is rs1010(G), with an odds ratio of 1.75 (CI: 1.17–2.62). Furthermore, this SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 possible risk variant...
Frequency: 48.7%
References:12
References:12
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discussed in this blog postA region of chromosome 9p21 has revealed numerous SNPs correlated with risk of myocardial infarction in a study of 2,000+ patients. This SNP, rs10116277, is highly correlated (r<sup>2</sup>=0.9) with rs2383207, as well as rs1333040 (r<sup>2</sup>=0.67). Ultimately, though, the SNP in this study (and region) with the highest disease correlation is rs10757278. According to a DeCode report, the G allele of his SNP is associated with lower risk of abdominal aortic aneurysm (AAA). [OMIM:?]
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associated with myocardial infarction
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rs7025486(A) was associated with up to a 20% increased risk of the various vascular diseases, with an odds ratio of 1.21 for abdominal aortic aneurysm (AAA) (p = 4.6x10-10), 1.18 for early onset myocardial infarction (MI) (p = 3.1x10-5), 1.14 for peripheral arterial disease PAD (p = 3.9x10-5), and 1.2 for pulmonary embolism (PE) (p = 00030), but it was not associated with intracranial aneurysm or ischemic stroke. An individual who carried two copies of this allele would have around a 44% increased risk of AAA. No association was seen between the A allele and common risk factors for arterial and venous disease—smoking, lipid levels, obesity, type 2 diabetes, and hypertension. theheart.org DeCode reports that the rs7025486(A;A) genotype is associated with 1.21x odds of peripheral arter...
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Coronary Heart Disease [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 controls; Replication Sample Size: 9,746 cases, 9,746 controls); (Region: 21q22.11; Reported Gene(s): SLC5A3, MRPS6, KCNE2; Risk Allele: rs9982601-T); (p-value= 0.00000000006).This variant is associated with Myocardial infarction (early onset).] [GWAS:Coronary artery disease]
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23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 Coronary Heart Disease [GWAS:Coronary Heart disease]
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rs2331291 a non-coding RNA, MIAT, that confers risk of Myocardial infarction.
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[GWAS:Body mass index]
Repute:Bad
References:38
References:38
~1.2x increased risk for heart disease
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rs10757274 is a SNP located in chromosomal region 9p21; to date (2009), it is the strongest genetic predictor of early myocardial infarction (heart attack) discovered so far. SNPs in this region are also associated with increased risk of stroke, abdominal aortic aneurysm (AAA), and intracranial aneurysm. Based on a large (20,000+) study primarily of Caucasian females, it appears that on its own, this single SNP does not improve on the discrimination or classification of predicted heart disease risk achieved by traditional risk factors, high-sensitivity C-reactive protein, and a family history of premature myocardial infarction. rs10757274 and rs2383206 can double the risk of heart diseaseAbout one in every four Caucasians are thought to carry the gene variants. rs10757278] in the same regi...
References:3
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rs17222842, also known as SG13S35, is an ALOX5AP gene SNP that has been defined as part of a haplotype potentially associated with risk for myocardial infarction or ischemic stroke. Details of this haplotype and several related studies are on the ALOX5AP page.
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Genetics of coronary artery disease: focus on genome-wide association studies. Genetics of diabetes complications. Genetic susceptibility to coronary heart disease in type 2 diabetes: 3 independent studies. [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 controls; Replication Sample Size: 9,746 cases, 9,746 controls); (Region: 6p24.1; Reported Gene(s): PHACTR1; Risk Allele: rs12526453-C); (p-value= 0.000000001).This variant is associated with Myocardial infarction (early onset).] [GWAS:Myocardial infarction (early onset)]
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A study of 858 cases concluded that SNPs in the intron of the CYP2J2 gene were associated with increased risk for myocardial infarction. rs11572325 had an odds ratio of 1.27, CI: 1.08-1.51, p=0.006. [PharmGKB:Curated The A allele of this intronic SNP is associated with a 1.27-fold increased risk of myocardial infarction relative to the T allele. This SNP is not associated with ischemic stroke risk.]
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rs12316150, a SNP also known as +1071, is located in the 3' untranslated region of the oxidized low density lipoprotein (lectin-like) receptor 1 OLR1 gene, which is also known as the LOX-1 gene. The rs12316150 risk allele has been associated with increased risk for Alzheimer's disease in several studies of ~200 Southern Italian Alzheimer patients, but only within the context of a haplotype including one or both of neighboring SNPs rs1050283 and rs669.
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
1.24x increased myocardial infarction risk, 1.29x increased aneurysm risk
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A common variant on chromosome 9p21 affects the risk of myocardial infarction, and is further discussed in this blog post 23andMe blog aneurysm *rs700651 2 G 1.18x risk 1.56x risk *rs10958409 8 A 1.37x risk 1.79x risk *rs1333040 9 T 1.29x risk 1.67x risk Brain Aneurysm [PharmGKB:Non-Curated GWAS results: Susceptibility loci for intracranial aneurysm in European and Japanese populations. (Initial Sample Size: 1,580 European cases, 6,276 European controls; Replication Sample Size: 495 Japanese cases, 676 Japanese controls); (Region: 9q21.3; Reported Gene(s): CDKN2A, CDKN2B; Risk Allele: rs1333040-T); (p-value= 0.0000000001).This variant is associated with Intracranial aneurysm.] [OMIM:ANEURYSM, INTRACRANIAL BERRY, 6] [GWAS:Intracranial aneurysm]
Magnitude: 0
Frequency: 69.0%
References:14
Frequency: 69.0%
References:14
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23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 Genetic susceptibility to coronary heart disease in type 2 diabetes: 3 independent studies. Genetics of diabetes complications. Using a latent growth curve model for an integrative assessment of the effects of genetic and environmental factors on multiple phenotypes. Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoids: a genome-wide association study. Genetics of coronary artery disease: focus on genome-wide association studies. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to...
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23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 Coronary Heart Disease [PharmGKB:Curated GWAS results: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. (Initial Sample Size: 2,967 cases, 3,075 controls; Replication Sample Size: 9,746 cases, 9,746 controls); (Region: 2q33.1; Reported Gene(s): WDR12; Risk Allele: rs6725887-C); (p-value= 0.00000001).This variant is associated with Myocardial infarction (early onset).] [GWAS:Myocardial infarction (early onset)]
common in clinvar you have the common genotype, but rare genotype has a beneficial effect on blood pressure and risk of myocardial infarction.
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[OMIM:MYOCARDIAL INFARCTION, DECREASED SUSCEPTIBILITY TO]
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rs4769874, also known as SG13S89, is an ALOX5AP gene SNP that has been defined as part of a haplotype potentially associated with risk for myocardial infarction or ischemic stroke. Details of this haplotype and several related studies are on the ALOX5AP page.
normal
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rs662799 is a SNP in the APOA5 gene. The rarer rs662799(C) allele has been associated in multiple reports (cited below) to be associated with higher triglyceride levels. Independently of triglyceride levels, perhaps, a study based on 1,864 Italian patients <45 years old at the time of their first heart attack (myocardial infarction) concluded that this SNP is associated with higher risk for an early heart attack, with a per C allele odds ratio of 1.44 (CI: 1.23-1.69, p = 6.7 × 10(-5)). This SNP has also been reported to help prevent weight gain from high fat diets. 1,073 men and 1,207 women participating in the Framingham Offspring Study rs662799 -1131T>C in modulates the effect of fat intake on BMI and obesity risk in both men and women. Individuals with at least one C allele g...
normal
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rs1800888, also known as Ile164, is a SNP in the beta 2 adrenergic receptor ADRB2 gene. The rs1800888(T) encodes the much rarer Ile allele. In a study of 330 patients undergoing percutaneous coronary intervention (PCI), patients carrying a rs1800888(T) allele showed a higher incidence of new acute myocardial infarction (17.5% vs. 4.5%, p = 0.001), new PCI (37.5% vs. 13.1%, p < 0.0001), and cardiac death (10% vs. 3.1%, p = 0.036). Regression analysis identified rs1800888(T) as an independent predictor of cardiac death (odds ratio 3.731, CI: 1.004 - 13.867, p = 0.049) and an overall major adverse cardiac event (odds ratio 4.1, CI: 1.945 - 8.640, p = 0.0001). A replication study was done on a population of 150 patients with peripheral artery disease. The presence of the rs1800888(T) allele...
common in complete genomics
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23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 Coronary Heart Disease [GWAS:Hematological and biochemical traits]
Magnitude: 0
References:3
References:3
common for Caucasians on the 23andme platform
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rs17222814, also known as SG13S25, is an ALOX5AP gene SNP that has been defined as part of a haplotype potentially associated with risk for myocardial infarction or ischemic stroke. Details of this haplotype and several related studies are on the ALOX5AP page. rs17222814 on bifurcation intima-media thickness and alcohol consumption exceeding 30 grams per day
1 genoset 43 snps
(hide) Myopia
decreased high myopia risk Less risk of high myopia (in French people). 34.2% of French people without high myopia have T here, but only 21.1% of controls do.(table)
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Formerly known as the very well studied rs1982073 [PharmGKB:Curated In conjunction with polymorphism at codon 25, defines high-, medium- or low-producer haplotype; Pro allele has been associated with higher levels of circulating TGFB1; Cystic Fibrosis patients who are C homozygotes may have increased risk of severe pulmonary disease; association found of C allele with increased risk of invasive breast cancer; associated with bone mineral density and genetic susceptibility to osteoporosis in Japanese adolescents and postmenopausal women; C allele may be involved in development of EBV-related diseases;C allele associated with increased risk for esophageal squamous cell carcinoma in Chinese; T allele associated with familial vesicoureteral reflux; C allele associated with increased severity ...
Frequency: 13.3%
References:1
References:1
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High myopia is not associated with the SNPs in the TGIF, lumican, TGFB1, and HGF genes. Genetic evidence implicating multiple genes in the MET receptor tyrosine kinase pathway in autism spectrum disorder. Association of polymorphisms in the hepatocyte growth factor gene promoter with keratoconus.
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Despite two previous GWAS studies associating this SNP with high myopia in Japanese populations, no association was seen in a Chinese population studied. [GWAS:Myopia (pathological)]
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The T allele appears to be protective against high myopia. [GWAS:Migraine]
1.6x increased risk for high myopia in Japanese (but not Chinese)
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In a study of more than 500 Japanese patients with high myopia, the rs2839471(T) allele was associated with higher risk. The odds ratio is 1.68 (p=0.00027). Despite two previous GWAS studies associating this SNP with high myopia in Japanese populations, no association was seen in a Chinese population studied.
References:1
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Candidate gene and locus analysis of myopia.
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Genetic and epigenetic factors at COL2A1 and ABCA4 influence clinical outcome in congenital toxoplasmosis. Host genetic and epigenetic factors in toxoplasmosis.
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myopia
Magnitude: 0
Frequency: 62.8%
Repute:Good
References:3
Frequency: 62.8%
Repute:Good
References:3
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The association of single nucleotide polymorphisms in the 5'-regulatory region of the lumican gene with susceptibility to high myopia in Taiwan. High myopia is not associated with the SNPs in the TGIF, lumican, TGFB1, and HGF genes. The association of haplotype at the lumican gene with high myopia susceptibility in Taiwanese patients. Association of lumican gene with susceptibility to pathological myopia in the northern han ethnic chinese.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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A systematic meta-analysis of genetic association studies for diabetic retinopathy.
common in complete genomics
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Noncoding mutations of HGF are associated with nonsyndromic hearing loss, DFNB39.
30 snps
(hide) Myotonia congenita
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Myotonia congenita rs80356706
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Myotonia congenita rs80356702
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Myotonia congenita rs121912805
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Myotonia congenita rs80356696
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
6 snps
(hide) Narcolepsy
HLA-DRB1*1501 carrier; higher multiple sclerosis risk Rs3135391(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.
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rs3135391 is highly correlated with the HLA-DRB1*1501 allele. The risk allele (T), is associated with a 3 to 6 fold higher risk for developing multiple sclerosis, and is the most significantly associated risk factor for MS. [PMC2892470] In one study, for example, the odds ratio was reported to be 3.04 (p < 1 x 10e-78). The HLA-DRB1*1501 allele has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and possibly narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. [PMC2892470] An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis would be to ensure...
1.3x higher risk of narcolepsy compared to (A;G) genotype
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Common variants in P2RY11 are associated with narcolepsy. Found that rs2305795 G allele appears to lower the risk of narcolepsy. This SNP is also in the intronal area of the EIF3G gene.
3x higher risk of multiple sclerosis Rs3135388(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.
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rs3135388(T) is highly (> 99%) correlated with the HLA-DRB1*1501 allele; the risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. The risk per allele (or per haplotype) appears additive. It has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and, when linked with DQB1*0602, narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. Note: most publications refer to the risk allele as rs3135388(A), but in dbSNP and SNPedia orientation, it is rs3135388(T). An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis ...
1.94x increased risk for narcolepsy
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rs1154155 is a SNP in the TCRA T-cell receptor alpha gene. The minor allele is (G). A study of 1,830 people with narcolepsy and cataplexy (a sudden loss of muscle tone that can cause people to collapse) compared to 2,164 healthy controls concluded that several SNPs in the TCRA gene were linked. The most significant association was with this SNP, rs1154155, with an average allelic odds ratio of 1.69 (genotypic odds ratios 1.94 and 2.55, p < 10e-21). Note the following, though, as quoted from a Science News article: 'Even with all of the known genetic risk factors, including the newly discovered version of the T cell receptor gene, a person has only a 1.5 percent chance of developing narcolepsy.... That suggests that, while narcolepsy is probably an autoimmune disorder, further genetic an...
Frequency: 25.7%
Repute:Bad
References:2
Repute:Bad
References:2
1.79x increased risk for narcolepsy in Europeans and 1.34x in Asians
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23andMe blog Each copy of the G version of rs12587781 increased the odds of narcolepsy by 1.79 times in Europeans and 1.34 times in Asians. The G version of rs12587781 showed a trend towards increased odds of narcolepsy for African Americans, but the results were not statistically significant. [OMIM:?]
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[GWAS:Narcolepsy]
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[GWAS:Narcolepsy]
normal
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rs5770917, a SNP located between the CPT1B and CHKB genes, was associated with narcolepsy in study of 222 Japanese individuals with narcolepsy and 389 Japanese controls, with replication of top hits in 159 Japanese individuals with narcolepsy and 190 Japanese controls, followed by the testing of 424 Koreans, 785 individuals of European descent and 184 African Americans. The risk allele rs5770917(C) had an odds ratio of 1.79 (p = 4.4 x 10e-7) in Japanese subjects and an odds ratio of 1.40 (p = 0.02) in other ancestry groups. Note that rs5770917 is in tight linkage (r2 > 0.93) with several nearby SNPs: rs2269382 and rs2269381. HLA-DQB1*0602 and relevance to Narcolepsy related to vaccination [PharmGKB:Non-Curated GWAS Results: Variant between CPT1B and CHKB associated with susceptibility ...
8 snps
(hide) Nephrotic syndrome
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:0
Frequency: 98.2%
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
2 snps
(hide) Neuroblastoma
2.8x higher risk of aggressive neuroblastoma
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Each G allele has been associated with an allelic odds ratio of 1.68 (p = 8.65 x 10(-18)) for risk of aggressive neuroblastoma. [OMIM:NEUROBLASTOMA]
complex; generally greater risk for cancer progression
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rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and H131R. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...
1.3x increased risk for neuroblastoma
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rs110419 is a SNP in the LMO1 LIM domain only 1 (rhombotin 1) gene. A GWAS study of 2,000+ patients (and 6,000+ controls) concluded that the rs110419(A) allele is associated with increased risk for neuroblastoma, with an allelic odds ratio of 1.34 (CI: 1.25–1.44, combined p = 5.2?×?10e?16). [GWAS:Neuroblastoma]
2.8x higher risk of aggressive neuroblastoma
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23andMe blog Each copy of a G at this SNP increases the odds of aggressive neuroblastoma by 1.68 times. allelic odds ratio of 1.68 (p = 2.74 x 10(-16)) Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. [OMIM:NEUROBLASTOMA] [GWAS:None]
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[GWAS:Neuroblastoma]
2x increased risk for neuroblastoma
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SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs9295536(A;A) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.93, CI: 1.55 to 2.40, p=8 x 10<sup>-8</sup>). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. For more information on this cluster of SNPs, see rs6939340. [OMIM:NEUROBLASTOMA] [GWAS:Neuroblastoma]
normal
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SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs4712653(C;C) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.96, CI: 1.57 to 2.43, p=7 x 10<sup>-8</sup>). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. For more information on this cluster of SNPs, see rs6939340. Common variations in BARD1 influence susceptibility to high-risk neuroblastoma. [OMIM:NEUROBLASTOMA] [GWAS:None]
2x increased risk for neuroblastoma
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SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs6939340(G;G) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.97, CI: 1.58 to 2.45, p=9.3 x 10<sup>-15</sup>). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. Presumably driven primarily by the at-risk homozygotes, the rs6939340(G) allele was considered to be a risk factor, however, there was insufficient data to conclude whether rs6939340(A;G) heterozygotes were actually at any increased risk compared to rs6939340(A;A) 'wild-type' homozygotes. ...
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[GWAS:Neuroblastoma]
Frequency: 42.5%
References:3
References:3
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[GWAS:Neuroblastoma]
Frequency: 85.8%
References:1
References:1
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[GWAS:Neuroblastoma]
11 snps
(hide) Nicotine dependence
Magnitude: 3
Frequency: 15.9%
Repute:Bad
References:102
Frequency: 15.9%
Repute:Bad
References:102
higher risk for nicotine dependence, lower risk for cocaine dependence
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Associated with smoking phenotype (p=0.007) based on association study of 2,000+ individuals, and functional studies demonstrated that the risk allele decreased response to a nicotine agonist, therefore the rs16969968(A) allele is likely to be involved in nicotine dependence. In a study 500+ individuals with cocaine dependence, the same rs16969968(A) allele was associated with a 0.67x decreased risk (p = 0.0045). A study of 200 individuals replicated the association between this SNP and nicotine dependence, and also concluded that the rs16969968(A) allele was significantly associated with 'enhanced pleasurable responses' to a person's first cigarette. 23andMe blog 23andMe considers rs1051730 equivalent The association between rs16969968 and lung cancer may, in part, be confounded by chroni...
1.8x increased risk of lung cancer; reduced response to alcohol, therefore possibly increased risk of alcohol abuse
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rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...
Frequency: 21.5%
References:2
References:2
normal?
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rs10485057 is a SNP in the opioid receptor, mu 1 OPRM1 gene. A study of 688 Caucasian smokers (and non-smoking controls) indicated that the rare rs10485057(G) allele was associated with higher likelihood of smoking initiation and nicotine dependence.
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Associated with nicotine Dependence as part of several haplotypes, based on a study of 1,000+ subjects including both African-Americans and European-Americans. The risk haplotype varies between populations. Among African-Americans, the haplotype C-C-G of rs2491397-rs2184026-rs3750344 had a significant positive association with nicotine dependence. Among European-Americans, for rs1435252-rs3780422-rs2779562-rs3750344, the C-A-C-A haplotype was positively associated with nicotine dependence while the T-A-T-A haplotype was negatively associated. [OMIM:GAMMA-AMINOBUTYRIC ACID B RECEPTOR 2; GABBR2]
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[PharmGKB:Non-Curated GWAS Results: Novel genes identified in a high-density genome wide association study for nicotine dependence (Initial Sample Size: 1,050 cases, 879 controls; Replication Sample Size: NR; Risk Allele: rs2836823-T).] [GWAS:Nicotine dependence]
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Associated with Nicotine Dependence as part of several haplotypes, based on a study of 1,000+ subjects including both African-Americans and European-Americans. Interestingly, the risk allele varies between populations. Among African-Americans, the haplotype C-C-G of rs2491397-rs2184026-rs3750344 had a significant positive association with nicotine dependence. Among European-Americans, for rs1435252-rs3780422-rs2779562-rs3750344, the C-A-C-A haplotype was positively associated with nicotine dependence while the T-A-T-A haplotype was negatively associated. [OMIM:GAMMA-AMINOBUTYRIC ACID B RECEPTOR 2; GABBR2]
associated with heavier smoking in Caucasians
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rs3003609 is a SNP in the dynamin 1 DNM1 gene. The (T) allele of rs3003609 is associated with heavier smoking and thus nicotine dependence, at least in Caucasians though perhaps not African-Americans, based on a study of 600+ families.
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Variations in this snp have been linked to nicotine dependence [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16874522&query_hl=3&itool=pubmed_docsum]
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[PharmGKB:Non-Curated GWAS Results: Novel genes identified in a high-density genome wide association study for nicotine dependence (Initial Sample Size: 1,050 cases, 879 controls; Replication Sample Size: NR; Risk Allele: rs4142041-G).] [GWAS:Nicotine dependence]
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Associated with nicotine Dependence as part of several haplotypes, based on a study of 1,000+ subjects including both African-Americans and European-Americans. The risk haplotype varies between populations. Among African-Americans, the haplotype C-C-G of rs2491397-rs2184026-rs3750344 had a significant positive association with nicotine dependence. Among European-Americans, for rs1435252-rs3780422-rs2779562-rs3750344, the C-A-C-A haplotype was positively associated with nicotine dependence while the T-A-T-A haplotype was negatively associated. [OMIM:GAMMA-AMINOBUTYRIC ACID B RECEPTOR 2; GABBR2]
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Associated with nicotine Dependence as part of several haplotypes, based on a study of 1,000+ subjects including both African-Americans and European-Americans. The risk haplotype varies between populations. Among African-Americans, the haplotype C-C-G of rs2491397-rs2184026-rs3750344 had a significant positive association with nicotine dependence. Among European-Americans, for rs1435252-rs3780422-rs2779562-rs3750344, the C-A-C-A haplotype was positively associated with nicotine dependence while the T-A-T-A haplotype was negatively associated. [OMIM:GAMMA-AMINOBUTYRIC ACID B RECEPTOR 2; GABBR2]
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Variations in this snp have been linked to nicotine dependence
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Variations in this snp have been linked to nicotine dependence [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16874522&query_hl=3&itool=pubmed_docsum]
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Associated with nicotine Dependence as part of several haplotypes, based on a study of 1,000+ subjects including both African-Americans and European-Americans. The risk haplotype varies between populations. Among African-Americans, the haplotype C-C-G of rs2491397-rs2184026-rs3750344 had a significant positive association with nicotine dependence. Among European-Americans, for rs1435252-rs3780422-rs2779562-rs3750344, the C-A-C-A haplotype was positively associated with nicotine dependence while the T-A-T-A haplotype was negatively associated. [OMIM:GAMMA-AMINOBUTYRIC ACID B RECEPTOR 2; GABBR2]
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identifies a region associated with nicotine dependence in this particular study (1,050 dependents, 879 non-dependent controls, all of European descent), noted as distinct from the loci which rs16969968 defines Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs. Variants in nicotinic receptors and risk for nicotine dependence. Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research. Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. Association of a single nucleotide polymorphism in neuronal...
normal
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rs6280, also known as '''Ser9Gly''', is a SNP in the dopamine receptor D3 DRD3 gene. The rs6280(C) allele encodes a glycine, and the (T) allele encodes a serine (in dbSNP orientation). In a study of 88 patients being treated for schizophrenia with olanzapine, those who were rs6280(C;C) homozygotes had greater positive symptom remission (endpoint rating of minimal or none on all PANSS clinical response positive items, 39.1%), as compared with (C;T) or (T;T) genotypes (13.8%; p = 0.033). Ser9Gly has been implicated in executive function in some studies, but the results are conflicting. * Gly/Gly carriers showed significantly (p = 0.002) poorer performance than Ser/Ser carriers on executive functioning tasks in a somewhat small Caucasian sample (84 patients with first-episode psychosis and 85...
common in complete genomics
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Associated with nicotine Dependence as part of several haplotypes, based on a study of 1,000+ subjects including both African-Americans and European-Americans. The risk haplotype varies between populations. Among African-Americans, the haplotype C-C-G of rs2491397-rs2184026-rs3750344 had a significant positive association with nicotine dependence. Among European-Americans, for rs1435252-rs3780422-rs2779562-rs3750344, the C-A-C-A haplotype was positively associated with nicotine dependence while the T-A-T-A haplotype was negatively associated. [OMIM:GAMMA-AMINOBUTYRIC ACID B RECEPTOR 2; GABBR2]
normal
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rs4648317, a SNP in the dopamine D2 receptor DRD2 gene, has been linked to higher rates of smoking and higher nicotine dependence scores, based on a study of ~220 adolescents. The risk allele rs4648317(T).
18 snps
(hide) Niemann-Pick disease
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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relevance to ebola? *rs28942106: C *rs28942108: A *rs28940897: G *https://www.23andme.com/you/community/thread/32901/ *http://www.livescience.com/47203-ebola-how-people-survive.html Another marker linked with people's ability to survive Ebola is a gene called human leukocyte antigen-B, which makes a protein that is important in the immune system. A 2007 study found that people with certain versions of this gene, called B*07 and B*14, were more likely to survive Ebola, while people with other versions, called B*67 and B*15, were more likely to die. Sequence-based human leukocyte antigen-B typing of patients infected with Ebola virus in Uganda in 2000: identification of alleles associated with fatal and nonfatal disease outcomes. [OMIM:[[Niemann-Pick disease]], TYPE C1, JUVENILE FORM]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
7 snps
(hide) Non-Hodgkin Lymphoma
MI risk, aspirin resistance 23andMe blog lower odds of early stent thrombosis
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The 'A2' allele of the platelet specific alloantigen system is encoded by rs5918(C), and it has been implicated as increasing the risk of myocardial infarctions, heart disease, and resistance to blood-thinning benefits of aspirin. On its own, the A2 allele is implicated especially in early onset heart disease ; in combination with the 4G allele of the PAI1 gene, rs1799889, the increased risk of myocardial infarction in a Finnish study population was 4 fold higher (odds ratio = 4.5, p=0.001), particularly in males (odds ratio = 6.4, p=0.0005) . Olympic skater Sergei Grinkov, who had this risk factor, died of a heart attack at age 28. A2 allele carriers also appear to be relatively resistant to the anti-thrombotic (i.e. anti-clotting) actions normally associated with aspirin] use. A protecti...
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rs3132453, a SNP in the BAT2 gene also known as V1883L, is associated with reduced risk for developing Non-Hodgkin Lymphoma based on a study of 458 patients. The odds ratio is 0.64 (CI: 0.45-0.90, p<0.01).
normal
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rs4833103 is a SNP located in a cluster of toll-like receptor genes. In a pooled analysis including three population-based case-control studies of Non-Hodgkin's lymphoma (1,946 cases, 1,808 controls), two SNPs in moderate linkage disequilibrium were significantly associated with NHL: rs10008492 (odds ratio for (C;T) genotype 1.12, CI: 0.97-1.30; OR(T;T) 1.40, CI: 1.15-1.71; p(trend)=0.001) and rs4833103 (OR(A;C) 0.75, CI: 0.64-0.88; OR(A;A) 0.74, CI: 0.62-0.90; p(trend)=0.002; p(dominant)=0.0002).
Frequency: 38.1%
Repute:Good
References:1
Repute:Good
References:1
normal
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rs10008492 is a SNP located in a cluster of toll-like receptor genes. In a pooled analysis including three population-based case-control studies of Non-Hodgkin's lymphoma (1,946 cases, 1,808 controls), two SNPs in moderate linkage disequilibrium were significantly associated with NHL: rs10008492 (odds ratio for (C;T) genotype 1.12, CI: 0.97-1.30; OR(T;T) 1.40, CI: 1.15-1.71; p(trend)=0.001) and rs4833103 (OR(A;C) 0.75, CI: 0.64-0.88; OR(A;A) 0.74, CI: 0.62-0.90; p(trend)=0.002; p(dominant)=0.0002). The impact of divergence time on the nature of population structure: an example from Iceland. Sequence variants in the TLR4 and TLR6-1-10 genes and prostate cancer risk. Results based on pooled analysis from three independent studies. Association of polymorphisms in TLR genes and in genes of the...
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A US study of 1,172 lymphoma patients and 982 controls looked at 57 SNPs in 36 immune function genes. Five SNPs in two cytokine genes, TNF and LTA, were associated with a 1.31x increase in Non-Hodgkin Lymphoma (OR, 1.31; 95% CI, 1.06-1.63; P = 0.01) and with a 1.64x increase in the subtype known as diffuse large B cell lymphoma (OR, 1.64; 95% CI, 1.23-2.19; P = 0.0007). The other four SNPS are listed below. The cytokine genes affect inflammatory and innate immune responses. * rs1800629 * rs361525 * rs1799724 * rs909253 [OMIM:LYMPHOTOXIN-ALPHA; LTA]
Normal risk for NHL. The minor, protective allele is rare.
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Non-Hodgkin's lymphoma rs4648022) was associated with NHL risk overall (ordinal OR, 0.59; 95% CI, 0.41-0.84; P(trend) = 0.0037)
7 snps
(hide) Nonalcoholic fatty liver disease
increased liver fat, odds of alcoholic liver disease
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rs738409 is a SNP in the PNPLA3 gene. In all HapMap populations the most common allele is a C on the plus strand, which means a G on the minus strand as represented for this SNP in dbSNP and in SNPedia. In the scientific literature, however, most authors appear unaware that this SNP is defined as oriented on the minus strand, so they refer incorrectly to rs738409(G) as the minor allele. The genotypes defined in SNPedia are correct for the minus orientation of this SNP, but this can be confusing since it's the opposite of what the literature indicates in many cases. In a Mestizo population, rs738409 is strongly associated with alcoholic liver disease and clinically evident alcoholic cirrhosis (unadjusted odds ratio 2.25, p=1.7e-10); ancestry-adjusted OR 1.79, p=1.9 x 10(-5)). rs738409(G) in...
complex! see rs4880
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The rs4880(T) allele, part of the codon for amino acid valine at codon 16 of the antioxidant protein from the mitochrondrial superoxide dismutase 2 SOD2 gene, is the most common in most populations studied. The rs4880(C) allele gives rise to an alanine at this position is it also known as Val16Ala manganese superoxide dismutase, or A16V. There appears to be some conflict in the literature over the effect of this SNP. Having a valine at codon 16 is said to reduce enzyme activity , and thus lead to increased oxidative stress, yet in at least one study of the actual enzyme levels measured in people, SOD2 activity was 33% higher in (C;T) or (T;T) individuals compared to (C;C) individuals . Regardless of how this resolves, several phenotypic associations have been reported for this SNP, includi...
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[PharmGKB:Curated This promoter variant is associated with hyperlipidemia (elevated triglyceride levels) for HIV-infected individuals treated with ritonavir.] [OMIM:?]
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[PharmGKB:Curated This promoter variant is associated with hyperlipidemia (elevated triglyceride levels) for HIV-infected individuals treated with ritonavir.] [OMIM:?]
common in complete genomics
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rs2228603 is a SNP in the ''NCAN'' gene (also known as ''CSPG3''), coding for the neurocan core protein. The T risk allele results in a proline to serine missense mutation at position 92 of the protein. In a large GWAS of individuals of European descent published in March, 2011, rs2228603 was found to be associated with nonalcoholic fatty liver disease (NAFLD), as evidenced by hepatic steatosis found by CT scanning and confirmed by histology. The investigators confirmed their initial findings with using the same case cohort and two separate control groups and found genome-wide significant odds ratios of 1.65 (95% CI = 1.15-2.87; p=5.29E-5; p=6.82E-10) and 1.9 (95% CI not reported) NAFLD is associated with higher LDL-C and lower LDL-C levels as well as impaired fasting glucose and increased...
common in complete genomics
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rs10508266 and rs3750861 shows significant association with lung cancer risk rs3750861 affects expression of KLF6 splicing variants in prostate cancer and we found that its rare allele is associated with reduced lung cancer risk
6 snps
(hide) Obesity
some risk linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil).
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
Alcohol Flush: Normal, doesn't flush. Normal hangovers. Normal risk of Alcoholism. Normal risk of Esophageal Cancer. Disulfiram is effective for alcoholism. Two working copies of Aldehyde Dehydrogenase (ALDH2) mean you won't turn bright red when you drink alcohol, unlike most Asians. After your body turns alcohol into the dangerous acetaldehyde, this gene quickly turns the acetaldehyde into vinegar. It also stops the acetaldehyde in cigarettes from causing Esophageal Cancer. It reduces hangovers compared to Asians, but less hangovers and flushing obviously increases the risk of alcoholism. Alcoholism can be treated effectively with the drug Disulfiram (Antabuse) which would stop this gene from working and cause the Asian flush in non-Asians. PMC2659709 [http://www.ncbi.nlm.nih.gov/pmc/art...
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rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Disulfiram (...
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
lower risk of obesity and Type-2 diabetes
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rs9939609 is a SNP in the fat mass and obesity associated FTO gene, aka the 'Fat Gene' The original paper describing it is here . [http://www.alzforum.org/new/detail.asp?id=1567 The researchers identified 10 different FTO SNPs in the first intron of the gene that associated with both BMI and type-2 diabetes. Because they all correlated with each other, they chose to examine one of the SNPs (rs9939609) in detail. rs9939609 has also been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.34 (CI 1.17-1.52), and for homozygotes, 1.55 (CI 1.3-1.84). In a different study, this SNP was found in a linkage block in the FTO gene with rs1121980; see rs1121980 for the association of th...
0.90x reduced risk of obesity
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rs7568369, also known as -963C>A, is a SNP in the Kruppel-like factor 7 KLF7 gene. A study of 14,818 Danish individuals with obesity found that the rs7568369(T) allele reduced obesity risk (odds ratio 0.90, CI: 0.84-0.96, p=0.001) and in studies of quantitative traits (n=5,535), this allele was associated with decreased body mass index (p=0.002) and waist circumference (p=0.003).
Frequency: 0.9%
References:3
References:3
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[GWAS:None]
Frequency: 1.8%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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obesity abdominal fat area in Korean women rs3811787 and rs1800592
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
None
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rs6013029 is a SNP in the CTNNBL1 gene. Found no evidence of early onset obesity or increased body mass index association with this SNP in several populations (~3,000 cases overall) of Central European (German) ancestry. While the older a study of ~1,900 Caucasians turned up associations between several SNPs in the CTNNBL1 gene and increased risk for obesity, of which rs6013029 was statistically the strongest, with an odds ratio of 1.42 for (T;T) homozgyotes compared to (G;G) homozygotes. This SNP achieved experiment-wise p values of 2.69 x 10<sup>-7</sup> for body mass index (BMI) and of 4.99 x 10<sup>-8</sup> for fat mass, respectively. The rs6013029(T) allele confers an average increase in BMI and fat mass of 2.67 kg/m(2) and 5.96 kg, respectively, compared to rs...
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[GWAS:Body mass index]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity (extreme)]
Frequency: 10.6%
References:6
References:6
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[GWAS:None]
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[GWAS:Obesity-related traits]
Frequency: 10.6%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 11.5%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 12.4%
References:34
References:34
if obese, dieting more effective
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rs17300539, also known as -11391 G/A, is a SNP in the promoter of the adiponectin ADIPOQ gene. A small study of 180 Spanish patients with obesity concluded that rs17300539(G;G) individuals are at increased risk of insulin resistance and MetS complications compared to carriers of an (A) allele. The rs17300539(A) allele confered protection from weight regain, particularly at 32-60 weeks after the low-calorie dietary intervention, when improvement in GG subjects had disappeared adiponectin levels and risk of diabetes rs17300539 P(n) = 2.6 x 10(-8) and rs822387 (P(n) = 3.8 x 10(-5) [OMIM:?]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 14.2%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Body mass index]
Frequency: 14.2%
References:1
References:1
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[GWAS:Obesity-related traits]
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P = 3.54 × 10(-9); OR = 1.14 association with childhood obesity
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 16.8%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 16.8%
References:1
References:1
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[GWAS:Obesity-related traits]
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[PharmGKB:Non-Curated GWAS results: Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. (Initial Sample Size: 32,387 individuals; Replication Sample Size: 59,092 individuals); (Region: 20p12.3; Reported Gene(s): BMP2; Risk Allele: rs2145270-T); (p-value= 0.000006).This variant is associated with Body mass index.] [GWAS:Body mass index]
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[GWAS:None]
Frequency: 17.7%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 19.5%
References:1
References:1
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Nominally associated to Weight in . [GWAS:Quantitative traits]
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[GWAS:Obesity-related traits]
Frequency: 19.5%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 20.4%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 20.4%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Weight]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Body mass index]
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[GWAS:Obesity-related traits]
Frequency: 21.6%
References:1
References:1
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[GWAS:Obesity-related traits]
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rs9568856; P = 1.82 × 10(-9); odds ratio (OR) = 1.22) association with childhood obesity
Frequency: 22.1%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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This SNP is in a linkage block in the FTO gene with rs1121980; see rs1121980 for the association of this block with early onset obesity since it showed the strongest association. [GWAS:None]
Frequency: 24.8%
References:1
References:1
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[GWAS:Obesity-related traits]
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linked to obesity [OMIM:LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 5; LRP5]
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[GWAS:Obesity-related traits]
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Association analysis of the FTO gene with obesity in children of Caucasian and African ancestry reveals a common tagging SNP. Common SNPs in FTO gene are associated with obesity related anthropometric traits in an island population from the eastern Adriatic coast of Croatia. [GWAS:Obesity (extreme)]
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Weight being the quantitative trait associated with in [GWAS:Quantitative traits]
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[GWAS:Obesity-related traits]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project (Initial Sample Size: 1,341 individuals (Framingham); Replication Sample Size: NR). This variant is associated with BMI.] [GWAS:BMI]
Frequency: 26.5%
References:1
References:1
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[GWAS:Obesity]
Frequency: 26.5%
References:1
References:1
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[GWAS:Obesity]
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In 'Association of the ADRA2A polymorphisms with the risk of type 2 diabetes: a meta-analysis.' a meta-analysis of publications prior to September 2012 showed no overall association between rs553668 and T2D risk, but did find an association with very high (poor) P-value for Europeans under recessive gene model (GT=AA, OR=1.36, p=0.02, 95% CI: 1.05, 1.76). In 'Genetic association of adrenergic receptor alpha 2A with obesity and type 2 diabetes.' rs553668 was found to correlate with obesity in Swedish population, but not significantly for BMI-corrected T2D risk. ADRA2A is involved in sympathetic nervous system's inhibition of insulin secretion and lipolysis, so direct effect on T2D is usually sought, but the Swedish study suggest it could work through body mass. It also mentions that rs55366...
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[GWAS:Obesity-related traits]
Frequency: 27.4%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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Adiponectin Levels
Frequency: 28.3%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 29.5%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[PharmGKB:Non-Curated The analyses of genome-wide association data from 1,380 Europeans with early-onset and morbid adult obesity and 1,416 age-matched normal-weight controls found an association of this variant (rs1424233) near MAF for risk of pooled childhood and adult severe obesity.] [OMIM:BODY MASS INDEX; BMI] [GWAS:Obesity]
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[GWAS:Body mass index]
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[GWAS:Obesity-related traits]
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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Weight being the quantitative trait associated with in [GWAS:Quantitative traits]
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[GWAS:Obesity-related traits]
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[GWAS:Body mass index]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 33.6%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 33.6%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 34.5%
References:2
References:2
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[GWAS:Weight]
Frequency: 34.5%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Body mass index]
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[OMIM:SYNDECAN 3; SDC3]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
normal
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rs1800587, also known as C-889T, is a SNP in the IL-1 alpha IL1A gene. A study of 556 adults in the Western Australian coronary heart disease (CHD) population concluded that rs1800587(T;T) homozygotes had larger waist circumference, by 1.8cm on average, compared to major allele (C;C) homozygotes. This association was even more pronounced in patients with higher levels of obesity or inflammatory markers. rs1800587 increases susceptibility to Intervertebral disc disease 1.31 times for (C;T) heterozygotes and 7.87 times for (T;T) homozygotes This SNP has also been reported to be associated with Alzheimer's disease in a few studies, but probably ruled out in even more studies, such as this one . Gene-environment interaction effects on the development of immune responses in the 1st year of life...
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[GWAS:Obesity-related traits]
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Adiponectin Levels
1.8x higher risk for obesity if in haplotype
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A study of 391 overweight patients concluded that the haplotype of rs1554483(G) and rs4864548(A) was associated with a 1.8-fold higher risk (CI: 1.31-2.54, p < 0.001) of obesity.
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Weight]
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[GWAS:Obesity-related traits]
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association with obesity Obesity: Preliminary Research Measures of Obesity
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[GWAS:Obesity-related traits]
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rs4917 is thought to regulate body fat levels and insulin sensitivity. see obesity link1 the MET/MET genotype has been previously linked with reduced plasma lipid levels and lower body fat concentrations. link2 Homozygosity for the rs2593813:G-rs4917:Met-rs4918:Ser haplotype conferred an increased risk for leanness (odds ratio=1.90, P=0.027). [OMIM:ALPHA-2-HS-GLYCOPROTEIN; AHSG]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 38.9%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 38.9%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
?
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rs7566605 was initially reported as being associated in at least 4 independent populations as being associated with obesity however replications are inconsistent, and a recent (2009) large meta-analysis comprising 34 studies (and over 70,000 subjects) has concluded that there is no evidence for overall association of the rs7566605 polymorphism with obesity. See also: Poster At least one population has since been reported in which this association was not seen. Furthermore, a study of 18,000 Danish subjects also failed to find any direct role for this SNP in the development of obesity, except that among physically inactive subjects, (C)-allele carriers tended to have a higher body mass index (by O.5 kg/m2) than (G)-allele carriers. On the other hand, a report has also been published indicat...
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[GWAS:Obesity-related traits]
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[GWAS:Obesity]
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rs10049088, rs1482853, rs17451107 and rs900400 are in strong linkage disequilibrium (r2>0.93) with each other. reports from the study itself and drawing from previous studies and meta-analysis that while rs900400 is strogly associated with birth adiposity (sum of skinfolds), that association doesn't bear over to childhood adiposity or adulthood BMI . This somewhat remarkable because childhood adoposity is known to be associated with adverse metabolic outcomes , but according to present studies rs900400 is not responsible for them , its effects disappearing by 3 months of age . The chromosome 3q25 locus associated with fetal adiposity is not associated with childhood adiposity [OMIM:?] [GWAS:Birth weight]
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Adiponectin Levels
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 40.2%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 40.7%
References:8
References:8
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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI. Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants? Common body mass index-associated variants confer risk of extreme obesity. Obesity genotype score and cardiovascular risk in women with type 2 diabetes mellitus. Novel obesity risk loci do not determine distribution of body fat depots: a whole-body MRI/MRS study. From monogenic to polygenic obesity: recent advances. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweig...
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[GWAS:Obesity-related traits]
Frequency: 41.0%
References:20
References:20
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obesity and type-2 diabetes *rs1121980 *rs7498665 *rs4752856 *rs17782313 *rs2815752 *rs10938397 The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI. Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants? Common body mass index-associated variants confer risk of extreme obesity. Obesity genotype score and cardiovascular risk in women with type 2 diabetes mellitus. Novel obesity risk loci do not determine distribution of body fat depots: a whole-body MRI/MRS study. From monogenic to polygenic obesity: recent advances. Genetic markers of adult obesity risk are associated with greater early infancy weight gain and growth. Obesity and diabetes genes are ...
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[GWAS:Obesity]
Frequency: 41.6%
References:1
References:1
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[GWAS:Body mass index]
Frequency: 41.6%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 41.6%
References:3
References:3
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[PharmGKB:Non-Curated GWAS results: Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. (Initial Sample Size: 32,387 individuals; Replication Sample Size: 59,092 individuals); (Region: 15q25.2; Reported Gene(s): RKHD3; Risk Allele: rs12324805-C); (p-value= 0.000007).This variant is associated with Body mass index.] [GWAS:Body mass index]
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[GWAS:Obesity-related traits]
Frequency: 42.0%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 42.0%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 42.5%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 42.5%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 42.5%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity]
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[GWAS:Obesity]
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[GWAS:Obesity-related traits]
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Although somewhat lacking in statistical power, several reports have linked rs1205, a UTR mutation known as CRP4 in the C-reactive protein CRP to the autoimmune disorder SLE, systemic lupus erythematosus. The risk allele in dbSNP orientation is (T). C-reactive protein (CRP) levels obesity rs1205(G) allele had significantly higher CRP levels than noncarriers in a dose-dependent manner suggesting a possible association with fat localization 23andMe blog each rs1205(T) lowered CRP by 20% but no association with heart disease. Analysis of polymorphisms in 16 genes in type 1 diabetes that have been associated with other immune-mediated diseases. A prospective assessment of the Y402H variant in complement factor H, genetic variants in C-reactive protein, and risk of age-related macular degenerat...
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[PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 16q12.2; Reported Gene(s): FTO; Risk Allele: rs6499640-A); (p-value= 0.00000000000006).This variant is associated with Weight.] [GWAS:Body mass index]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 12q13.13; Reported Gene(s): BCDIN3D, FAIM2; Risk Allele: rs7138803-A); (p-value= 0.0000002).This variant is associated with Weight.] [GWAS:Body mass index]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 43.8%
References:1
References:1
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[GWAS:Obesity-related traits]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 1p31.1; Reported Gene(s): NEGR1; Risk Allele: rs2568958-A); (p-value= 0.00000000001).This variant is associated with Body mass index.] [GWAS:Body mass index]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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obesity and type-2 diabetes *rs1121980 *rs7498665 *rs4752856 *rs17782313 *rs2815752 *rs10938397 Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants? Common body mass index-associated variants confer risk of extreme obesity. Novel obesity risk loci do not determine distribution of body fat depots: a whole-body MRI/MRS study. From monogenic to polygenic obesity: recent advances. A strategy for analyzing gene-nutrient interactions in type 2 diabetes. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study. FTO and MC4R gene variants are associated with obesity in polycystic ovary syndrome. Genetic predictors of weight loss and weig...
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[GWAS:Obesity-related traits]
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[GWAS:Obesity]
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[GWAS:Obesity-related traits]
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Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study. [PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 6p21.33; Reported Gene(s): AIF1, NCR3; Risk Allele: rs2844479-T); (p-value= 0.00000002).This variant is associated with Weight.] [GWAS:Weight]
Frequency: 45.5%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Body mass index]
Frequency: 46.0%
References:1
References:1
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[GWAS:Obesity]
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[GWAS:Obesity-related traits]
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source rs1477196 and rs1861868 associated with obesity ine subjects with low physical activity scores and no effect on those with above-average physical activity scores. Physical activity and the association of common FTO gene variants with body mass index and obesity. Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3.
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[GWAS:Obesity-related traits]
Frequency: 46.4%
References:1
References:1
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[GWAS:Obesity-related traits]
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'We studied a population-based sample of Caribbean-origin Hispanics (n = 920, aged 45-74 y) living in the Boston area. Obesity measures (waist and hip circumference, BMI) did not differ between GG subjects and carriers of the A allele (GA and AA). In multivariate linear regression models, we found a significant interaction between complex carbohydrate intake as a continuous variable and PLIN 11482 G > A genotype for waist circumference (P = 0.002). By dichotomizing complex carbohydrate intake, we found significantly different effects across PLIN 11482G > A genotypes. When complex carbohydrate intake was <144 g/d, waist circumference was larger in PLIN 11482G > A carriers (P = 0.024). Conversely, when complex carbohydrate intake was >/=144 g/d, waist and hip circumferences we...
Frequency: 46.9%
References:6
References:6
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Replication and extension of genome-wide association study results for obesity in 4923 adults from northern Sweden. Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants? Common body mass index-associated variants confer risk of extreme obesity. Obesity genotype score and cardiovascular risk in women with type 2 diabetes mellitus. Novel obesity risk loci do not determine distribution of body fat depots: a whole-body MRI/MRS study. From monogenic to polygenic obesity: recent advances. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study. FTO and MC4R gene variants are associated with obesity in polycystic ovary syndrome. [Pharm...
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rs6996321 significantly related to spine bone mineral density (p=0.002) and rs10914367 associated with hip BMD (p=0.028). Non-vertebral fracture risk was significantly increased in carriers of 'A' allele of rs9900972 (OR=2.06, p=0.0187) Interferon regulatory factor 6 (IRF6) and fibroblast growth factor receptor 1 (FGFR1) contribute to human tooth agenesis. A genome-wide linkage scan for cleft lip and cleft palate identifies a novel locus on 8p11-23.
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[GWAS:Obesity]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 47.8%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 47.8%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 47.8%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Body mass index]
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[GWAS:Obesity-related traits]
Frequency: 48.2%
References:1
References:1
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[GWAS:Obesity (extreme)]
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[GWAS:Body mass index]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 19q13.11; Reported Gene(s): KCTD15, CHST8; Risk Allele: rs29941-C); (p-value= 0.000000005).This variant is associated with Weight.] [GWAS:Body mass index]
Frequency: 48.7%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 48.7%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 48.7%
References:4
References:4
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5,261 obese individuals with 14,106 controls, all of European descent. This snp is in on the 23andMe microarray, and reported as equivalent to ones reported in and . (T;T) linked to 1.12 times higher odds of obesity compared to individuals with the (C;T) genotype, and those with the (C;C) genotype had about 1.12 times lower odds of obesity. Obesity: Preliminary Research Measures of Obesity [GWAS:Body mass index]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity]
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[GWAS:Obesity-related traits]
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rs1800949 and rs943003 showed suggestive evidence for association with adult-onset morbid obesity in Finns
Frequency: 49.6%
References:1
References:1
(hide)
[GWAS:Body mass index]
Frequency: 49.6%
References:2
References:2
(hide)
[GWAS:Body mass index]
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[GWAS:Obesity-related traits]
1.8x higher risk for obesity if in haplotype
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A study of 391 overweight patients concluded that the haplotype of rs1554483(G) and rs4864548(A) was associated with a 1.8-fold higher risk (CI: 1.31-2.54, p < 0.001) of obesity.
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SNP rs1550922 has been associated with both glucose levels and body-mass index (eg obesity) in the Framingham Heart Study datasets, and is thus associated with heart disease. source
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source rs1477196 and rs1861868 associated with obesity in subjects with low physical activity scores and no effect on those with above-average physical activity scores. Physical activity and the association of common FTO gene variants with body mass index and obesity. The genetics of obesity: FTO leads the way. [Association of FTO gene polymorphisms and morbid obesity in the population of Extremadura (Spain)]. [Association of FTO Polymorphisms with Obesity and Obesity-Related Outcomes in Portuguese Children].
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 50.8%
Repute:Bad
References:60
Repute:Bad
References:60
increased type-2 diabetes risk; higher gestational diabetes risk
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rs10830963 was associated with an increased risk of type-2 diabetes in our Han Chinese cohort (OR 1.16, 95% CI 1.03-1.31, p = 0.015). As previously described, the risk variant was also associated with increased fasting plasma glucose, showing an increase of 0.068 mmol/l (95% CI 0.036-0.100, p = 4 x 10(-5)) per risk allele rs10830962, rs4753426, and rs10830963 were significantly associated with higher fasting plasma glucose concentrations and reduced OGTT- and IVGTT-induced insulin release. rs3781638 displayed significant association with lower fasting plasma glucose levels and increased OGTT-induced insulin release A study totaling 19,000+ Europeans concluded that rs10830963 had the most influence of any MTNR1B gene SNP on the risk for type-2 diabetes. Specifically, the (G) allele increase...
Frequency: 51.3%
References:8
References:8
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rs10830962, rs4753426, and rs10830963 were significantly associated with higher fasting plasma glucose concentrations and reduced OGTT- and IVGTT-induced insulin release. rs3781638 displayed significant association with lower fasting plasma glucose levels and increased OGTT-induced insulin release [GWAS:None]
Frequency: 51.3%
References:1
References:1
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[GWAS:Body mass index]
Frequency: 51.3%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Body mass index]
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summary, indicating a small effect of this SNP, seen only in meta-analyses rs3792267 associated with noninsulin-dependent diabetes mellitus, polycystic ovary syndrome, type 2 diabetes, gestational diabetes and obesity [OMIM:CALPAIN 10; CAPN10]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 51.4%
References:1
References:1
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[GWAS:Weight]
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[GWAS:Obesity (extreme)]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity]
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[PharmGKB:Non-Curated The analyses of genome-wide association data from 1,380 Europeans with early-onset and morbid adult obesity and 1,416 age-matched normal-weight controls found an association of this variant (rs1805081) in NPC1 for risk of pooled childhood and adult severe obesity.] [OMIM:BODY MASS INDEX; BMI] [GWAS:Obesity]
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CYP19A1 genetic polymorphisms may be associated with obesity related phenotypes in Chinese women.
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[GWAS:Obesity-related traits]
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[GWAS:Obesity (extreme)]
Frequency: 53.1%
References:1
References:1
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[GWAS:Obesity]
Frequency: 53.1%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 53.1%
References:1
References:1
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[GWAS:Obesity (extreme)]
Frequency: 53.1%
References:2
References:2
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[GWAS:Monocyte chemoattractant protein-1]
Frequency: 53.1%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Adiponectin levels]
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[GWAS:Obesity-related traits]
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Recapitulation of genome-wide association studies on body mass index in the Korean population. [GWAS:None]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 5q23.2; Reported Gene(s): NR; Risk Allele: rs2115172-A); (p-value= 0.000002).This variant is associated with Weight.] [GWAS:Weight]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[OMIM:?] [GWAS:None]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 55.8%
References:2
References:2
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Common body mass index-associated variants confer risk of extreme obesity. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. [PharmGKB:Non-Curated GWAS results: Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. (Initial Sample Size: 32,387 individuals; Replication Sample Size: 59,092 individuals); (Region: 11p15.4; Reported Gene(s): STK33; Risk Allele: rs10769908-C); (p-value= 0.000001).This variant is associated with Body mass index.] [GWAS:Body mass index]
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[GWAS:Homocysteine levels]
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[GWAS:Obesity-related traits]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 1p21.3; Reported Gene(s): NR; Risk Allele: rs1973993-C); (p-value= 0.000001).This variant is associated with Weight.] [GWAS:Weight]
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[GWAS:None]
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[GWAS:Obesity-related traits]
Frequency: 57.5%
References:1
References:1
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[GWAS:Obesity-related traits]
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rs1800949 and rs943003 showed suggestive evidence for association with adult-onset morbid obesity in Finns
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[GWAS:Body mass index]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 58.4%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 58.4%
References:11
References:11
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Alzheimer's disease risk for non ApoE4 carriers is affected by the heterozygous form of rs6265, as well as the diplotypes of rs6265, rs11030104, and rs2049045. [GWAS:Body mass index]
Frequency: 58.4%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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SNP rs2286983 has been associated with both cholesterol levels and body-mass index (eg obesity) in the Framingham Heart Study datasets, and is thus associated with heart disease. source
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[GWAS:Obesity-related traits]
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rs6996321 significantly related to spine bone mineral density (p=0.002) and rs10914367 associated with hip BMD (p=0.028). Non-vertebral fracture risk was significantly increased in carriers of 'A' allele of rs9900972 (OR=2.06, p=0.0187) [GWAS:Obesity-related traits]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 11p14.1; Reported Gene(s): BDNF; Risk Allele: rs7481311-T); (p-value= 0.000003).This variant is associated with Weight.] [GWAS:Body mass index]
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[GWAS:Obesity-related traits]
Frequency: 61.9%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 62.8%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:None]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 64.6%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 65.6%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Obesity risk
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Obesity: Preliminary Research [PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 3q27.2; Reported Gene(s): SFRS10, ETV5, DGKG; Risk Allele: rs7647305-C); (p-value= 0.00000000007).This variant is associated with Body mass index.] [GWAS:Body mass index]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project (Initial Sample Size: 1,341 individuals (Framingham); Replication Sample Size: NR). This variant is associated with BMI.] [GWAS:BMI]
Frequency: 68.1%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
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[GWAS:Adiposity]
Frequency: 69.9%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 69.9%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 70.8%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 70.8%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 72.6%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 72.6%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 72.6%
References:1
References:1
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Occurs within the RFTN1 (Raftlin, lipid raft linker 1) gene [GWAS:Obesity (extreme)]
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[GWAS:Obesity-related traits]
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A meta-analysis of several APOA2 SNPs (including this one) found no association between any APOA2 SNPs studied and type-2 diabetes.
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[GWAS:Obesity (extreme)]
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[GWAS:Obesity-related traits]
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The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI. From monogenic to polygenic obesity: recent advances. The obesity gene, TMEM18, is of ancient origin, found in majority of neuronal cells in all major brain regions and associated with obesity in severely obese children. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study. Association study of common polymorphisms in MSRA, TFAP2B, MC4R, NRXN3, PPARGC1A, TMEM18, SEC16B, HOXB5 and OLFM4 genes with obesity-related traits among Portuguese children. [PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obe...
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[GWAS:Obesity-related traits]
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blog ENPP1 harbors a mutation with a derived state known to protect against obesity and type II diabetes27 that is present in 90% of non-Africans but virtually absent in Africans K121Q (rs1044498) The Q allele of ENPP1 K121Q is associated with hyperglycemia and insulin resistance in whites. increased fasting plasma glucose (FPG), A1C, fasting insulin, and insulin resistance by homeostasis model assessment (HOMA-IR; all P = 0.01-0.006). Association of ENPP1 gene polymorphisms with hand osteoarthritis in a Chuvasha population. Studies of the relationship between the ENPP1 K121Q polymorphism and type 2 diabetes, insulin resistance and obesity in 7,333 Danish white subjects. Common variants in the ENPP1 gene are not reproducibly associated with diabetes or obesity. ENPP1 K121Q polymorphism and...
Frequency: 75.2%
References:1
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 76.1%
References:1
References:1
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[GWAS:Obesity-related traits]
Frequency: 76.1%
References:1
References:1
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[GWAS:Obesity-related traits]
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This SNP may be related to obesity and diabetes. Genomic variants at the PINK1 locus are associated with transcript abundance and plasma nonesterified fatty acid concentrations in European whites. Near perfect linkage disequilibrium with rs622525. G allele is a proxy for rs622525(T) which is associated with higher PINK1 transcript levels.
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[GWAS:Obesity (extreme)]
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[GWAS:Obesity-related traits]
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[GWAS:Obesity-related traits]
Frequency: 77.9%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 78.8%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 78.8%
References:1
References:1
(hide)
[GWAS:Body mass index]
Frequency: 78.8%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 79.6%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 79.6%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Body mass index]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 80.5%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 80.5%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 82.0%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 82.1%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 82.3%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 85.0%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 85.0%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 85.0%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 85.8%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 86.2%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 86.5%
References:2
References:2
(hide)
[GWAS:Myopia (pathological)]
Frequency: 86.7%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 87.6%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 89.2%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 90.3%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 92.0%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 92.3%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 93.8%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 93.8%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 95.3%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 95.6%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 95.6%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
Frequency: 96.5%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 99.1%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 99.1%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
Frequency: 99.1%
References:1
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
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obesity abdominal fat area in Korean women rs3811787 and rs1800592
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[GWAS:Adiponectin levels]
Duffy-positive This genotype is associated with European populations and southwestern Native American populations.
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rs2814778 is within the DARC gene, which encodes the Duffy blood group antigen . This SNP shows an almost perfectly fixed difference in frequency between Europeans and those with African ancestry. (One exception appears to be a certain population of Czech gypsies, and certain non-Ashkenazi Jewish populations.) Additionally the Namibian San samples of the CEPH-HGDP are, uncharacteristically for Africans, all AA homozygotes for this SNP. The rs2814778 (G) allele is associated with African populations, while rs2814778 (A) is associated with European populations and southwestern Native American populations. rs2814778(G;G) protect against Plasmodium vivax malaria and predicts of white blood cell and neutrophil count 23andMe blog discussion Malaria Resistance (Duffy Antigen) [PharmGKB:Curated A...
References:1
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[GWAS:Obesity-related traits]
References:2
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[GWAS:Monocyte chemoattractant protein-1]
References:1
(hide)
[GWAS:Obesity-related traits]
(hide)
[GWAS:Obesity-related traits]
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The T allele of this SNP is associated with higher risk of pancreatic cancer. Phosphodiesterase 8B gene variants are associated with serum TSH levels and thyroid function. Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. Genetic variants associated with Von Willebrand factor levels in healthy men and women identified using the HumanCVD BeadChip. [PharmGKB:Non-Curated GWAS results: Population-based genome-wide association studies reveal six loci influencing plasma levels of live...
References:4
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rs33977706, also known as -820G>T, is a SNP in the promoter region of the suppressor of cytokine signalling 1 SOCS1 gene. This SNP has been reported to be associated with body mass index and obesity.
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Pleiotropic effects of GIP on islet function involve osteopontin. Genetic variation in the glucose-dependent insulinotropic polypeptide receptor modifies the association between carbohydrate and fat intake and risk of type 2 diabetes in the Malmo Diet and Cancer cohort. [PharmGKB:Curated Risk or phenotype-associated allele: A . Phenotype 1: In a meta-analysis of nine genome-wide association studies (n = 15,234 nondiabetic individuals) and a follow-up of 29 independent loci (n = 6,958-30,620), this SNP was found to be associated with 2-h glucose level (a clinical measure of glucose tolerance). Effect (s.e.m.) = 0.09(0.01) mmol/l per A allele. Study size/population/ethnicity: 15,234 plus 6,958-30,620 nondiabetic individuals of European descent. Significance metric(s): p = 1.98 x 10(-15). Ph...
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Within the FTO gene, many SNPs appear to be co-inherited. The SNP showing the strongest association with body weight (i.e. body mass index, BMI) is not rs8043757, although this SNP is one of co-inherited SNPs in the FTO gene region. For more information, refer to the FTO gene or the most studied of FTO SNPs, rs9930506. [GWAS:Obesity]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project (Initial Sample Size: 1,341 individuals (Framingham); Replication Sample Size: NR). This variant is associated with BMI.] [GWAS:BMI]
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This SNP may be related to obesity and diabetes. Genomic variants at the PINK1 locus are associated with transcript abundance and plasma nonesterified fatty acid concentrations in European whites. T allele associated with higher PINK1 transcript levels. Near perfect linkage disequilibrium with rs3131713.
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[GWAS:Obesity-related traits]
normal obesity risk
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rs1421085 is a SNP located in the first intron of the FTO (fat mass and obesity associated) gene on chromosome 16. This SNP showed the most association with obesity in the original work by Dina et al . Moreover, it is located in a conserved region. Within the FTO gene, many SNPs appear to be co-inherited. The SNP showing the strongest association with body weight (i.e. body mass index, BMI) is not rs1421085, although this SNP is one of co-inherited SNPs in the FTO gene region. For more information, refer to the FTO gene or the most studied of FTO SNPs, rs9930506. However, in one study of 583 extremely obese women with several FTO SNPs, the strongest association was indeed with rs1421085 (p=3.04x10<sup>-10</sup>, OR = 1.75, CI: 1.47-2.08). * Note: The three FTO SNPs, rs1421085, ...
Magnitude: 0
Frequency: 0.0%
References:4
Frequency: 0.0%
References:4
average
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rs1121980, a SNP in the FTO gene, showed the strongest association of several SNPs in the region with early onset obesity in a study of ~1,000 Caucasians. The odds ratio for the rs1121980(T) risk allele was 1.66 (CI: 1.37–2.01); and the odds ratios for heterozygotes and homozygotes (rs1121980(T;T)) were estimated (with a correct p<0.0001) at 1.67 (CI: 1.22–2.27) and 2.76 (CI: 1.88–4.03), respectively. Note that although rs1121980 showed the strongest association, it is in a block in the FTO gene of at least 5 other SNPs that are in linkage disequilibrium (r<sup>2</sup>>=0.88 for all). The other 5 SNPs are: * rs9939973 * rs7193144 * rs9940128 * rs8050136 * rs9939609 This SNP is also associated with (severe) obesity i...
normal
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This snp influences obesity however the most strongly linked neighboring snp is rs9939609. You probably want that one. This plos genetics paper reports rs9930506 showed the strongest association with BMI (p = 8.6 *10-7), hip circumference (p = 3.4 * 10-8) and weight (p = 9.1 * 10-7). homozygotes for the rare 'G' allele were were 1.3 BMI units heavier than homozygotes for the common 'A' allele. This SNP did not show any association with obesity, type-2 diabetes or any other related traits in a study of 3,210 Chinese subjects. Furthermore, the minor allele frequency was much lower in Chinese populations compared to populations of European descent. rs9930506 (A;A) showed decreased levels of methylated PPARGC1A in comparison with AG + GG genotypes, suggesting a potential role of promoter PPARG...
Magnitude: 0
Frequency: 25.7%
References:17
Frequency: 25.7%
References:17
normal
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Within the FTO gene, many SNPs appear to be co-inherited. The SNP showing the strongest association with body weight (i.e. body mass index, BMI) is not rs17817449, although this SNP is one of co-inherited SNPs in the FTO gene region. For more information, refer to the FTO gene or the most studied of FTO SNPs, rs9930506. A study of 900+ Quebec individuals reported that rs17817449 was associated with BMI (p=0.0014), weight (p=0.0059) and waist circumference (p=0.0021) under an additive model, and in addition, influenced fasting insulin (p=0.011) and HOMA-IR (p=0.038). * Note: The three FTO SNPs, rs1421085, rs17817449, and rs9939609, are in strong linkage disequilibrium (pairwise r<sup>2</sup>>0.97), and there are two primary haplotypes, C-G-A (42.0 %) and T-T-T (55.5 %). This ...
normal
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This SNP is in a linkage block in the FTO gene with rs1121980; see rs1121980 for the association of this block with early onset obesity since it showed the strongest association. This SNP did not show any association with obesity, type-2 diabetes or any other related traits in a study of 3,210 Chinese subjects. Furthermore, the minor allele frequency was much lower in Chinese populations compared to populations of European descent. However, a more recent study of 4,189 Chinese Han subjects combined with a meta-analysis of published studies concluded that rs8050136(A) was associated with both increased risk for type-2 diabetes and obesity. rs8050136 associated with increased food intake, but not of impaired energy expenditure. [PharmGKB:Non-Curated GWAS results: Genome-wide association yie...
common in clinvar
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obesity Q223R rs1137101 may be associated with obesity in women with a psychotic disorder treated with atypical antipsychotic drugs Gln223Arg polymorphism could be considered a disease susceptibility modulating factor both in ischemic heart disease or dilated cardiomyopathy patients. [OMIM:LEPTIN RECEPTOR POLYMORPHISM]
Magnitude: 0
Frequency: 38.9%
Repute:Good
References:2
Frequency: 38.9%
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 1p21.3; Reported Gene(s): NR; Risk Allele: rs10783050-C); (p-value= 0.000004).This variant is associated with Body mass index.] [GWAS:Body mass index]
normal risk
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rs5082 is a SNP in the apolipoprotein APOA2 gene, and may influence obesity and heart disease risk. Individuals homozygous for the -265T>C polymorphism in rs5082, i.e. individuals with the rs5082(C;C) genotype of the Apolipoprotein A-II gene (APOA2) promoter, are associated with increased Body Mass Index and food intake in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Study of ~1000 individuals. The odds ratio for obesity in (C;C) individuals compared to rs5082(T) allele carriers was 1.70 (CI: 1.02-2.80, p=0.039). Total energy, total fat, and total protein intake were all significantly higher in (C;C) individuals. In a separate study, a case-control analysis of 484 Australian male coronary artery disease patients concluded that rs5082(C;C) individuals were at significant...
Magnitude: 0
Frequency: 47.8%
References:23
Frequency: 47.8%
References:23
normal
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A study of 14,000 Indian Asian or Caucasian adults indicates that rs12970134(A) alleles are associated with obesity. The average increase in waist circumference is 0.9cm BMI units per risk allele. see also The common obesity variant near MC4R gene is associated with higher intakes of total energy and dietary fat, weight change and diabetes risk in women. Variants near MC4R are associated with obesity and influence obesity-related quantitative traits in a population of middle-aged people: studies of 14,940 Danes. Investigation of the locus near MC4R with childhood obesity in Americans of European and African ancestry. The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI. Large effects on body mass index and insulin resistanc...
common in complete genomics
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Obesity: Preliminary Research [PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 11p14.1; Reported Gene(s): BDNF; Risk Allele: rs925946-T); (p-value= 0.000000004).This variant is associated with Weight.] [GWAS:Body mass index]
Magnitude: 0
Frequency: 49.6%
Repute:Good
References:5
Frequency: 49.6%
Repute:Good
References:5
Magnitude: 0
Frequency: 50.4%
Repute:Good
References:90
Frequency: 50.4%
Repute:Good
References:90
normal
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A study of 60,000 adults indicates that rs17782313(C) alleles are associated with higher body mass index (BMI), with even greater effect in children. The average increase in BMI is 0.22 BMI units (p = 2.8 x 10<sup>-15</sup>). Note that rs10871777 is considered an equivalent SNP in Caucasian and Asian populations. The rs17782313(C) allele is equivalent to the rs10871777(G) allele. The rs17782313](C) allele is significantly associated with higher intakes of total energy and dietary fat. In addition, the SNP was related to greater long-term weight change and increased risk of diabetes in women. rs17782313(C) more snacking, however rs1421085(C) did not influence eating behavior obesity and type-2 diabetes *rs1121980 *rs7498665 *rs4752856 *rs17782313 *rs2815752 *rs10938397 [PharmGK...
slightly higher fat mass
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rs5746059 is a SNP in the tumor necrosis factor-alpha receptor 2 TNFRSF1B gene. A study of ~1,800 subjects from 400 Caucasian families concluded that carriers of a rs5746059(A) allele had a 4.6% higher fat mass and a 2.5% increased percentage fat mass compared to noncarriers; the results were significant after multiple testing correction. This same correlation was also seen in 700 independent Chinese Han adults and 1,000 additional Caucasians. This SNP therefore appears to be associated with risk for obesity.
Magnitude: 0
Frequency: 54.5%
Repute:Good
References:13
Frequency: 54.5%
Repute:Good
References:13
common in complete genomics
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The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI. Common body mass index-associated variants confer risk of extreme obesity. From monogenic to polygenic obesity: recent advances. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study. Physical activity attenuates the genetic predisposition to obesity in 20,000 men and women from EPIC-Norfolk prospective population study. [PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 1q25.2; Reported Gene(s):...
normal
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rs6971091 is a SNP on chromosome 7 that has been linked to obesity. In a study of 400+ patients, rs6971091(A) allele carriers had an odds ratio of at least 2 for obesity defined by both body mass index (BMI) and leptin levels.
normal
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rs1143634, also known as +3954, is a SNP in the IL-1 beta IL1B gene. A study of 556 adults in the Western Australian coronary heart disease (CHD) population concluded that rs1143634(T;T) homozygotes had larger waist circumference, by 1.8cm on average, compared to major allele (C;C) homozygotes. This association was even more pronounced in patients with higher levels of obesity or inflammatory markers. rs1143634 increases susceptibility to Alopecia Areata 2.67 times for heterozygotes (CT) and 1.13 times for homozygotes (TT) rs1143634 increases susceptibility to Alzheimer's disease 2.33 times for homozygotes (TT) rs1143634 increases susceptibility to Cervical lesions, low-grade squamous intraepithelial lesions 4.29 times for heterozygotes (CT) and 3.57 times for homozygotes (TT) rs1143634 in...
common/normal Val/val (normal) variant of the Val66Met snp in the BDNF gene that codes for brain-derived neurotrophic factor. Met/met is associated with susceptibility to neuropsychiatric disorders.
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. (Initial Sample Size: 80,969 individuals; Replication Sample Size: 11,036 individuals); (Region: 13q12.2; Reported Gene(s): NR; Risk Allele: rs7336332-G); (p-value= 0.000001).This variant is associated with Weight.] [GWAS:Weight]
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Obesity: Preliminary Research Measures of Obesity [PharmGKB:Non-Curated GWAS results: Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. (Initial Sample Size: 32,387 individuals; Replication Sample Size: 59,092 individuals); (Region: 2p25.3; Reported Gene(s): TMEM18; Risk Allele: rs6548238-C); (p-value= 0.000000000000000001).This variant is associated with Body mass index.] [OMIM:TRANSMEMBRANE PROTEIN 18; TMEM18] [GWAS:Body mass index]
Magnitude: 0
Frequency: 77.9%
References:1
Frequency: 77.9%
References:1
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[GWAS:Obesity (extreme)]
normal
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* Within the PFKP gene, rs6602024 showed very strong association with BMI (p = 4.9 * 10-6). Homozygotes for the rare 'A' allele of this SNP (minor allele frequency = 0.12) were 1.8 BMI units heavier than homozygotes for the common 'G' allele. * They did not replicate association between rs6602024 and obesity-related traits in the GenNet sample, although they found that in European Americans, Hispanic Americans and African Americans, homozygotes for the rare 'A' allele where, on average, 1.0 - 3.0 BMI units heavier than homozygotes for the more common 'G' allele. Furthermore, a study of 18,000 Danish subjects also failed to find any direct role for this SNP in the development of obesity. Genome-wide association scans identified CTNNBL1 as a novel gene for obesity. Tests for candidate-gene i...
Magnitude: 0
Frequency: 82.3%
Repute:Good
References:10
Frequency: 82.3%
Repute:Good
References:10
common on affy axiom data
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[PharmGKB:Non-Curated The analyses of genome-wide association data from 1,380 Europeans with early-onset and morbid adult obesity and 1,416 age-matched normal-weight controls found an association of this variant (rs10508503) near PTER for risk of pooled childhood and adult severe obesity.] [OMIM:BODY MASS INDEX QUANTITATIVE TRAIT LOCUS 8; BMIQ8] [GWAS:Obesity]
normal
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rs4994, also known as Trp64Arg or as the Arg64 variant, is a SNP in the ADRB3 gene. The rs4994(C) allele encodes the variant arginine. In a study of 600+ women initially referred for coronary angiography and then followed for 6 years, during which time 115 experienced a heart problem, rs4994(C) individuals were calculated to be at higher risk (adjusted hazard ratio 2.10, CI: 1.05-4.24). This risk was due to subtle increases in risk for all of the individual endpoints, and was only seen in women without obstructive coronary artery disease. Response to Diet and Exercise [PharmGKB:Curated Arg in position 64 associated with olanzapine-induced weight gain] [OMIM:OBESITY, SUSCEPTIBILITY TO]
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:1
Frequency: 85.0%
Repute:Good
References:1
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[GWAS:Obesity-related traits]
common in complete genomics
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23andMe blog rs2237892(C) is associated with an increased risk for developing type-2 diabetes. each C at rs2237892 increased the odds of type 2 diabetes by 1.4 times, compared to the TT genotype. It’s important to note, however, that the C version is actually pretty common. In Asian populations, the C version of rs2237892 increased a person’s odds of type 2 diabetes by 1.42 times compared to people with TT. But because about 50% of the Asian population is actually CT at this SNP, it could be viewed that CC has 1.3 times the odds compared to typical, while TT has 0.61 times the typical odds. In European populations, about 85% of people are CC. This means that the results of Yasuda et al really show that compared to most Europeans, people with CT at rs22...
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:5
Frequency: 85.8%
Repute:Good
References:5
Magnitude: 0
Frequency: 86.7%
Repute:Good
References:2
Frequency: 86.7%
Repute:Good
References:2
Magnitude: 0
Frequency: 87.6%
Repute:Good
References:1
Frequency: 87.6%
Repute:Good
References:1
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[GWAS:Obesity-related traits]
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[GWAS:Weight]
normal risk
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rs1528133, a SNP in the TUB gene, was found in a study of 492 unrelated type-2 diabetes patients to have a significant effect on body mass index and thus obesity (1.54 kg/m(2), p= 0.006). When two populations were combined, totaling ~1200 patients, the risk allele (rs1528133(C) averaged an increase of 0.54 kg/m2 (CI: –0.19-1.26). Two additional TUB SNPs, rs2272382, and rs2272383, mapping to the 3' end of the gene showed similar associations and were in linkage disequilibrium with rs1528133. A follow-up study of 1,680 middle-aged Dutch women found that this allele, rs1528133(C), was significantly associated with increased weight (+1.88 kg, p=0.022) and body mass index (+0.56 units, p= 0.05). rs1528133(C) carriers were also associated with an increased glycemic load of 1.8...
common in complete genomics
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*rs6232 G allele (in dbSNP orientation) linked to 1.34x increased risk of obesity *rs6234/rs6235 (or rs10515237) see also: spitoon Obesity: Preliminary Research [PharmGKB:Curated In a study at 13,659 individuals of European ancestry the N221D variant was consistently associated with obesity in adults and children.] [OMIM:PROPROTEIN CONVERTASE, SUBTILISIN/KEXIN-TYPE, 1; PCSK1]
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[GWAS:Obesity-related traits]
Magnitude: 0
Frequency: 92.0%
Repute:Good
References:1
Frequency: 92.0%
Repute:Good
References:1
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[GWAS:Obesity-related traits]
Magnitude: 0
Frequency: 92.0%
Repute:Good
References:2
Frequency: 92.0%
Repute:Good
References:2
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[GWAS:Obesity-related traits]
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[GWAS:Body mass index]
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[GWAS:Obesity-related traits]
normal
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rs662799 is a SNP in the APOA5 gene. The rarer rs662799(C) allele has been associated in multiple reports (cited below) to be associated with higher triglyceride levels. Independently of triglyceride levels, perhaps, a study based on 1,864 Italian patients <45 years old at the time of their first heart attack (myocardial infarction) concluded that this SNP is associated with higher risk for an early heart attack, with a per C allele odds ratio of 1.44 (CI: 1.23-1.69, p = 6.7 × 10(-5)). This SNP has also been reported to help prevent weight gain from high fat diets. 1,073 men and 1,207 women participating in the Framingham Offspring Study rs662799 -1131T>C in modulates the effect of fat intake on BMI and obesity risk in both men and women. Individuals with at least one C allele g...
normal
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rs2229616, a variant in the MC4R gene known as V103I, has been associated with appetite regulation, body mass index (and thus obesity), and other features of metabolic syndrome. The most common allele is rs2229616(G); the rarer (A) allele encodes the 103I (isoleucine), and this (A) allele has been associated in a study of 8,000+ Caucasians with a significantly decreased waist circumference (-1.46 cm, p = 0.020), decreased glycosylated hemoglobin (HbA1c) (-0.09%, p = 0.040), and increased HDL-cholesterol (HDL-C) (+1.76 mg/dl, P = 0.056), but no change in blood pressure. The odds of having three or more components of the metabolic syndrome were substantially reduced among carriers of an rs2229616(A) allele (odds ratio = 0.46, p = 0.003). Basically, rs2229616(A) carriers are on average slight...
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[GWAS:Obesity-related traits]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
common in complete genomics
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rs16964465 rs16964476 may influence the risk of obesity through possible regulation of hypothalamic neuropeptide secretion [OMIM:SECRETOGRANIN III; SCG3]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
common in complete genomics
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rs16964465 rs16964476 may influence the risk of obesity through possible regulation of hypothalamic neuropeptide secretion [OMIM:SECRETOGRANIN III; SCG3]
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[GWAS:Obesity-related traits]
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
average
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SNP rs1800437, located in the coding region of the GIPR gene and known as Glu354Gln, shows a marginal association with cardiovascular disease (CVD) in a study of ~200 patients from a Dutch population. Heterozygotes are reported to be at lower risk for CVD, with an odds ratio of 0.72 (CI: 0.52 - 0.97, p=0.03). However, no significant association was seen for homozygous carriers of the minor allele. [GWAS:Obesity]
normal
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rs266729 is a SNP in the adiponectin ADIPOQ gene that may help elucidate correlations between obesity and some types of cancer. Two case-control studies including colorectal cancer patients and controls were conducted; the first case involving 441 patients and 658 controls, all of Ashkenazi Jewish ancestry, and the second including 199 patients and 199 matched (sex, age and ethnicity) controls. rs266729(G) showed decreased colorectal cancer risk in both studies; in the first, with an odds ratio of 0.72 (CI:0.55-0.95) and in the second, with an odds ratio of 0.52 (CI: 0.34-0.78). Combining the two studies led to an overall decreased colorectal cancer odds ratio of 0.73 (CI: 0.53-0.99) for this allele.[http://blog.23andme.com/2008/09/30/snpwatch-genetic-link-between-obesity-and-colorectal-ca...
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[OMIM:OBESITY, EARLY-ONSET, SUSCEPTIBILITY TO]
452 snps
(hide) Obsessive compulsive disorder
normal
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rs4570625, also known as G-703T, is a SNP in the tryptophan hydroxylase 2 TPH2 gene. This SNP has been linked to several psychiatric and/or behavioural phenomena, including: * rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder * rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission * rs4570625(G;G) homozygosity was a significant predictor of clinical placebo response, being associated with greater improvement in anxiety symptoms. g2b2mh is rs4570625(G;G) is a significant predictor of clinical placebo response? maybe not panic disorder with a possible gender-dependent effect Transmission disequilibrium of polymorphic variants in the tryptophan hydroxylase-2 gene in attention-deficit/hyperactivity disorder. Associa...
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rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder Tourette's Syndrome
Frequency: 77.9%
References:1
References:1
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This SNP is located in the intronic region of the SLC1A1 transporter gene. While the mechanism is unknown, it is associated with Obsessive compulsive disorder (OCD). OCD is an anxiety disorder where symptoms include repetitive behaviors aimed at decreasing anxiety. SLC1A1 is a candidate gene that has been the focus of many studies. Elevated glutamate levels have been found in the cerebrospinal fluid of many OCD patients, and since SLC1A1 affects glutamate transport – it is a likely candidate for study. SLC1A1 is expressed in the brain, and OCD is associated with neural changes. Rs12682807 is located in chr9:4564022 in the intronic region. It is an A to C transition. A study looked at 21 SNPs in Europeans and originally found no correlation between rs12682807 and OCD (815 trios, 306 c...
may be part of a haplotype associated with OCD
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rs25532 is a SNP in a regulatory region upstream of the serotonin transporter SLC6A4 gene. The more common allele, rs25532(C), is the higher-expressing allele. A study of patients with obsessive compulsive disorder (OCD) concluded that the major allele of rs25532 was a major contributor to the association of a corresponding haplotype with this disorder. [PharmGKB:Curated This study found that the minor allele of the functional C > T single nucleotide polymorphism, rs25532, located less than 150 nucleotides centromeric of the serotonin transporter-linked polymorphic region indel (known as 5-HTTLPR) significantly decreased luciferase reporter gene expression levels by 15-80%, depending on 5-HTTLPR allele background and cell type.]
4 snps
(hide) Osteoarthritis
Increased risk of mental disorders
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rs16944 is a SNP in the interleukin 1, beta gene, a member of the cytokine family involved in the inflammatory response. The rs16944 G;G genotype is associated with risk for multiple mental illnesses. An increased risk for schizophrenia was found in a genetic association study of 2111 Caucasian individuals with an odds ratio of 1.24 (95% CI 1.09, 1.41) . Studies examining the brains of schizophrenic and bipolar individuals found reduced gray matter and hypoactivity associated with the G;G genotype. Additionally, this genotype is associated with impaired ability to achieve remission in a study of 256 Caucasian individuals with depression (odds ratio = 1.74; 95% confidence interval 1.2-4.3). The rs16944 A allele increases susceptibility to Osteoarthritis, with 1.80 times for heterozygotes (A...
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
Magnitude: 1.3
Frequency: 88.5%
Repute:Bad
References:1
Frequency: 88.5%
Repute:Bad
References:1
1.3x increased risk for osteoarthritis
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rs10947262(C) was found to be associated with increased risk for osteoarthritis among Japanese and Europeans, with an odds ratio of 1.32 (CI: 1.19-1.46, combined p = 6.73×10e-8). This SNP is also in linkage disequilibrium with rs7775228, which was found to be associated in Japanese with osteoarthritis. [GWAS:Knee osteoarthritis]
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[GWAS:Osteoarthritis]
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rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele in these positions increased the risk of disease (p=0.006 and, p=0.008, respectively). Carrying a haplotype with the G allele in all three promoter SNPs increased the risk of symptomatic DIP OA more than four-fold (OR 4.45, p=0.001). Carriage of the G-G diplotype indicated an increased risk of both symmetrical DIP OA (OR 1.52 95% CI 1.0...
normal One report indicates that rs419598(T;T) carriers, if they are also IL1B -511 heterozygotes, have an increased chance of surviving a bout of bacterial meningitis . The (T;T) genotype is the most common in all populations studied.
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May modulate other variations. Also known as the +2018T/C SNP. In a study of 113 Japanese patients with chronic periodontitis (CP), individuals with the rs419598(C) allele are at 0.29x lower CP risk (p = 0.016). IL1B -511 allele heterozygotes have a 4 fold higher chance of surviving bacterial meningitis than (either) homozygote . SO what's this have to do with rs419598? Odds of surviving meningitis apparently further increase 2X for IL1B -511 heterozygotes who are also rs419598(T;T), i.e. homozygous for IL1RN +2018 rs419598 (T) allele (the most common one; also known as '+8006'). Radiographic severity of knee osteoarthritis is conditional on Interleukin 1 Receptor Antagonist gene variations
Frequency: 48.7%
References:1
References:1
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[GWAS:Osteoarthritis]
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[GWAS:Osteoarthritis]
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Authors of this study of just 189 subjects conclude that rs3740199 polymorphism may affect occurrence of knee osteoarthritis and its progression (p = 0.018), and even speculate that this SNP's effect is 'remarkably gender-dependent and anatomical site-specific'. Of course, another alternative is that it's just another case of overinterpretation based on having too few samples for a properly powered SNP study. Only time will tell. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
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Radiographic severity of knee osteoarthritis is conditional on Interleukin 1 Receptor Antagonist gene variations
normal height
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rs6060369 is a SNP associated with a (slight) increase in height, in that individuals tend to be 0.44cm taller for each rs6060369(C) allele they carry. This finding was statistically significant (p=9.7x10e-7), and ultimately tested in over 28,000 individuals. A haplotype of rs6060369 and rs143383, a neighboring SNP in the GDF5 gene, can be defined, which also links height to osteoarthritis since rs143383 has previously been linked to osteoarthritis. Medpage article Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. Assessing the impact of global versus local ancestry in association studies. [PharmGKB:Non-Curated GWAS Results: Common variants in the GDF5...
normal
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rs7639618 is one of several SNPs in the DVWA gene found to be associated with osteoarthritis based on a study of several Japanese patient populations. The allelic odds ratio is 1.45 (CI: 1.27-1.65, p = 2.2 x 10e-8) for the minor allele, which is the (T) allele (in dbSNP orientation). Our results suggest that the effect that DVWA amino acid changes have on tubulin binding is unlikely to influence risk of OA in Caucasians. rs7639618 with knee osteoarthritis with an odds ratio (OR) of 1.29, 95% confidence interval (CI) of 1.15 -1.45 and P of 2.70x10(-5), but not for Europeans [OMIM:OSTEOARTHRITIS SUSCEPTIBILITY 6; OS6]
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rs7775228 is one of three HLA region SNPs used to tag the DQ2.2 haplotype in gs221. rs7775228(T) was found to be associated with increased risk for osteoarthritis among Japanese, but not Europeans, with an odds ratio of 1.34 (CI: 1.21-1.49, combined p = 2.43×10e?8). This SNP is also in linkage disequilibrium with rs10947262, which was found to be associated in multiple populations with osteoarthritis. 23andMe reports that the C allele at rs7775228 is associated with hay fever (allergic rhinitis and allergy to grass pollen. Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants. [GWAS:None]
common in complete genomics
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rs4140564, a SNP on chromosome 1 near the PTGS2 and PLA2G4A genes, has been associated with knee osteoarthritis. A study of 255 British patients, replicated subsequently in ~2,000 UK, Dutch and US patients, found that rs4140564 was associated with knee osteoarthritis in all populations studied with an overall odds ratio = 1.55, CI: 1.30-1.85, p < 6.9 x 10e-7. [PharmGKB:Curated GWAS results: Genome-wide Association Scan Identifies a Prostaglandin-Endoperoxide Synthase 2 Variant Involved in Risk of Knee Osteoarthritis (Initial Sample Size: 357 cases, 285 controls; Replication Sample Size: 1,177 cases, 2,372 controls). This variant is associated with Knee osteoarthritis.] [GWAS:Knee osteoarthritis]
normal
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rs11718863 is one of several SNPs in the DVWA gene found to be associated with osteoarthritis based on a study of several Japanese patient populations. The allelic odds ratio is 1.43 (CI: 1.26-1.63, p = 5.2 x 10e-8) for the minor allele, which is the (T) allele (in dbSNP orientation). Association of the DVWA and GDF5 polymorphisms with osteoarthritis in UK populations. Large replication study and meta-analyses of DVWA as an osteoarthritis susceptibility locus in European and Asian populations. [OMIM:OSTEOARTHRITIS SUSCEPTIBILITY 6; OS6]
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rs7775 (R324G) osteoarthritis at multiple joints (p = 0.07), particularly in the hip in women associated with osteoarthritis of the hip in females This is an arg324-to-gly (R324G) substitution Meta-analysis of 14 studies did not support a significant association between rs7775 and osteoarthritis. Functional variants within the secreted frizzled-related protein 3 gene are associated with hip osteoarthritis in females. Genetic variation in candidate osteoporosis genes, bone mineral density, and fracture risk: the study of osteoporotic fractures. No association of the polymorphisms of the frizzled-related protein gene with peak bone mineral density in Chinese nuclear families. Variant alleles of the Wnt antagonist FRZB are determinants of hip shape and modify the relationship between hip shap...
common in complete genomics appears to be common on the 23andMe platform
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rs1800796 IL-6 572G>C polymorphism (and h.211 haplotype) is associated with abdominal aortic aneurysm (AAA). The risk allele is C. Our results provide evidence that there is a clear genetic influence of IL6 -572C>G polymorphism on plasma levels of fibrinogen and CRP, but this polymorphism does not lead to elevated blood pressure. rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele ...
17 snps
(hide) Osteoporosis
Increased risk of mental disorders
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rs16944 is a SNP in the interleukin 1, beta gene, a member of the cytokine family involved in the inflammatory response. The rs16944 G;G genotype is associated with risk for multiple mental illnesses. An increased risk for schizophrenia was found in a genetic association study of 2111 Caucasian individuals with an odds ratio of 1.24 (95% CI 1.09, 1.41) . Studies examining the brains of schizophrenic and bipolar individuals found reduced gray matter and hypoactivity associated with the G;G genotype. Additionally, this genotype is associated with impaired ability to achieve remission in a study of 256 Caucasian individuals with depression (odds ratio = 1.74; 95% confidence interval 1.2-4.3). The rs16944 A allele increases susceptibility to Osteoarthritis, with 1.80 times for heterozygotes (A...
Frequency: 5.3%
References:2
References:2
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[GWAS:Bone mineral density (spine)]
Frequency: 11.5%
References:4
References:4
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[PharmGKB:Curated GWAS results: Genome-wide Association and Follow-Up Replication Studies Identified ADAMTS18 and TGFBR3 as Bone Mass Candidate Genes in Different Ethnic Groups. (Initial Sample Size: 1,000 white individuals; Replication Sample Size: 4,925 white individuals, 350 Chinese hip fracture cases, 350 Chinese controls, 2,955 Chinese individuals, 908 West African men); (Region: 16q23.1; Reported Gene(s): ADAMTS18; Risk Allele: rs11864477-C); (p-value= 0.00000002).This variant is associated with Bone mineral density.] [OMIM:BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 13; BMND13] [GWAS:Bone mineral density]
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[GWAS:Bone mineral density (spine)]
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[PharmGKB:Non-Curated GWAS results: New sequence variants associated with bone mineral density. (Initial Sample Size: 6,865 individuals; Replication Sample Size: 8,510 individuals); (Region: 17q21.31; Reported Gene(s): C17orf53; Risk Allele: rs227584-T); (p-value= 0.0000009).This variant is associated with Bone mineral density (hip).] [GWAS:Bone mineral density (hip)]
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news rs4355801, was associated with a 20% increased risk of osteoporosis (significant at P=0.038). At least one copy of the risk allele (A) of rs4355801 was found in 79% of study participants. Participants carrying at least one copy of each risk allele -- 22% of the study population -- had a 50% increased risk of osteoporosis, which was significant at P=0.0026, and a 29% increased risk of osteoporotic fractures (significant at P=0.014). rs3736228 associated with decreased bone mineral density (p=6.3x10(-12) for lumbar spine and p=1.9x10(-4) for femoral neck) and an increased risk of both osteoporotic fractures (odds ratio [OR] 1.3, 95% CI 1.09-1.52, p=0.002) and osteoporosis (OR 1.3, 1.08-1.63, p=0.008). rs4355801 associated with decreased bone mineral density (p=7.6x10(-10) for lumbar spi...
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rs9594738 increases susceptibility to Bone mineral density variations, lower for carriers of the T allele [PharmGKB:Non-Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 176. Study population/ethnicity: 87 European descent Caucasians and 89 Yorubans. Significance metric(s): p = 0.00001. Type of association: FA; GN.] [OMIM:BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 9; BMND9] [GWAS:None] [GWAS:Bone mineral density (hip)]
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news rs6469792 and rs6469804 association with bone mineral density. [PharmGKB:Non-Curated GWAS Results: Multiple Genetic Loci for Bone Mineral Density and Fractures (Initial Sample Size: 5,861 individuals; Replication Sample Size: 7,925 individuals; Risk Allele: rs6469804-A). This variant is associated with Bone mineral density (spine).] [OMIM:BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 10; BMND10] [GWAS:Bone mineral density (spine)]
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 176. Study population/ethnicity: 87 European descent Caucasians and 89 Yorubans. Significance metric(s): p = 0.000004. Type of association: FA; GN.] [OMIM:?] [GWAS:Bone mineral density (spine)]
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news rs6469792 and rs6469804 association with bone mineral density.
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This SNP, and/or perhaps neighboring SNPs around this 230 kb linkage block of chromosome 1q, influences bone mineral density and thus potentially osteoporosis risk based on a study of 1,300+ premenopausal Caucasian women (p=1.3x10<sup>-6</sup>)
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rs6993813 increases susceptibility to Bone mineral density variations, lower for carriers of the A allele rs6993813 increases susceptibility to Osteoporotic fractures for carriers of the A allele [PharmGKB:Non-Curated GWAS Results: Multiple Genetic Loci for Bone Mineral Density and Fractures (Initial Sample Size: 5,861 individuals; Replication Sample Size: 7,925 individuals; Risk Allele: rs6993813-C). This variant is associated with Bone mineral density (hip).] [OMIM:BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 10; BMND10] [GWAS:Bone mineral density (hip)]
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rs9525625 is in linkage disequilibrium with a polymorphism that increases susceptibility to Bone mineral density variations, lower for carriers of the C allele
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rs1038304 increases susceptibility to Bone mineral density variations, lower for carriers of the G allele [PharmGKB:Non-Curated GWAS results: New sequence variants associated with bone mineral density. (Initial Sample Size: 6,865 individuals; Replication Sample Size: 8,510 individuals); (Region: 6q25.1; Reported Gene(s): ESR1; Risk Allele: rs1038304-G); (p-value= 0.0000000004).This variant is associated with Bone mineral density (hip).] [OMIM:BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 11; BMND11] [GWAS:Bone mineral density (hip)] [GWAS:Bone mineral density (hip)]
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rs9594759 increases susceptibility to Bone mineral density variations, lower for carriers of the T allele Common variants in the region around Osterix are associated with bone mineral density and growth in childhood. Replication study of candidate genes/loci associated with osteoporosis based on genome-wide screening. Genome-wide association study identifies ALDH7A1 as a novel susceptibility gene for osteoporosis. Genetic variation in the RANKL/RANK/OPG signaling pathway is associated with bone turnover and bone mineral density in men. [PharmGKB:Non-Curated GWAS results: New sequence variants associated with bone mineral density. (Initial Sample Size: 6,865 individuals; Replication Sample Size: 8,510 individuals); (Region: 13q14.11; Reported Gene(s): RANKL; Risk Allele: rs9594759-T); (p-v...
Frequency: 29.2%
References:1
References:1
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The research paper suggests that the 3 snps rs17703883, rs12594287 and rs16964201 affect bone mineral density in men.
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[GWAS:Bone mineral density (hip)]
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[GWAS:Bone mineral density]
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rs2470152 is clearly associated with serum E2 and E1 levels in men, influencing risk of many conditions including prostate cancer, breast cancer and osteoporosis
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[GWAS:Bone mineral density]
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[GWAS:None]
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rs9479055 increases susceptibility to Bone mineral density variations, lower for carriers of the C allele Common variants in the region around Osterix are associated with bone mineral density and growth in childhood. Genome-wide association study identifies ALDH7A1 as a novel susceptibility gene for osteoporosis. Analysis of recently identified osteoporosis susceptibility genes in Han Chinese women.
increased osteoporosis risk
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rs7646054 is a SNP in the ARHGEF3 gene. A study of 769 Australian female siblings found that the rs7646054(G) allele was significantly associated with lower bone mineral density (BMD) and thus osteoporosis in an age-related manner. Significant associations with hip and spine BMD were confirmed (p = 0.003-0.038), as well as an association with fracture rate (p = 0.02). [PharmGKB:Curated In family-based association tests, five SNPs(of which rs7646054 showed the strongest association) demonstrated significant association with decreased age-adjusted bone mineral density. The initial findings were in women from Australia and the UK, and the association was replicated in a cohort of postmenopausal women from the UK.]
Frequency: 35.5%
References:1
References:1
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rs11155795 is in linkage disequilibrium with a polymorphism that increases susceptibility to Bone mineral density variations, lower for carriers of the G allele
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[GWAS:Bone mineral density (spine)]
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[PharmGKB:Non-Curated GWAS results: New sequence variants associated with bone mineral density. (Initial Sample Size: 6,865 individuals; Replication Sample Size: 8,510 individuals); (Region: 17q21.31; Reported Gene(s): SOST; Risk Allele: rs1513670-A); (p-value= 0.00000002).This variant is associated with Bone mineral density (hip).] [GWAS:Bone mineral density (hip)]
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[GWAS:Bone mineral density (hip)]
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rs3018362 increases susceptibility to Osteoporotic fractures for carriers of the A allele related to Paget’s disease of bone 23andMe blog. [OMIM:?] [GWAS:Paget's disease]
Frequency: 37.2%
References:1
References:1
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[GWAS:Osteoporosis]
Frequency: 38.1%
References:5
References:5
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[PharmGKB:Non-Curated GWAS results: New sequence variants associated with bone mineral density. (Initial Sample Size: 6,865 individuals; Replication Sample Size: 8,510 individuals); (Region: 12q13.13; Reported Gene(s): OSX; Risk Allele: rs10876432-A); (p-value= 0.0000001).This variant is associated with Bone mineral density (spine).] [OMIM:?] [GWAS:Bone mineral density (spine)]
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[OMIM:?] [GWAS:Bone mineral density (spine)]
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[GWAS:Bone mineral density]
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rs4869742 is in linkage disequilibrium with a polymorphism that increases susceptibility to Bone mineral density variations, lower for carriers of the T allele [GWAS:None]
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rs4870044 increases susceptibility to Bone mineral density variations, lower for carriers of the T allele [PharmGKB:Non-Curated GWAS Results: Multiple Genetic Loci for Bone Mineral Density and Fractures (Initial Sample Size: 5,861 individuals; Replication Sample Size: 7,925 individuals; Risk Allele: rs4870044-T). This variant is associated with Bone mineral density (spine).] [OMIM:BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 11; BMND11] [GWAS:Bone mineral density (spine)]
increases susceptibility to postmenopausal osteoporosis
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rs1062033 increases susceptibility to Osteoporosis, postmenopausal for carriers of the G allele Common variations in estrogen-related genes are associated with severe large-joint osteoarthritis: a multicenter genetic and functional study. [OMIM:CYTOCHROME P450, FAMILY 19, SUBFAMILY A, POLYPEPTIDE 1; CYP19A1]
Intermediate risk of low bone mineral density disorders
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rs1544410, also known as the BsmI polymorphism, is a SNP in the Vitamin D receptor (VDR). Multiple studies examining bone mineral density (BMD) in women have associated the A allele with increased risk of low BMD , , & . Additionally, A meta-analysis of 26 studies estimated a decreased risk of osteoporosis associated with the G;G genotype with an odds ratio of 0.61, 95% CI, 0.40-0.92 . rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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Associated with bone mineral density and thus osteoporosis in a Chinese population. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Genetic modulation of neural response during working memory in healthy individuals: interaction of glucocorticoid receptor and dopaminergic genes.
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[PharmGKB:Non-Curated GWAS results: New sequence variants associated with bone mineral density. (Initial Sample Size: 6,865 individuals; Replication Sample Size: 8,510 individuals); (Region: 2q12.1; Reported Gene(s): NR; Risk Allele: rs6735786-C); (p-value= 0.000002).This variant is associated with Bone mineral density (hip).] [GWAS:Bone mineral density (hip)]
Frequency: 46.9%
References:0
References:0
normal
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rs13357391 is a SNP in the - get ready - 'sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1' SPOCK1 gene. You gotta just love the names these fun-loving scientists come up with, don't ya? A study of 477 Caucasian women, followed up by replication studies in another ~1,600 and also 1,300+ Chinese women, found that several linked SNPs in the SPOCK1 gene are associated with age at menarche. rs13357391 replicated across all groups studied (p < 10e-3), with the minor (C) allele associated with a (slightly) earlier age at menarche.
normal
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rs1859345 is a SNP in the - get ready - 'sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1' SPOCK1 gene. A study of 477 Caucasian women, followed up by replication studies in another ~1,600 and also 1,300+ Chinese women, found that several linked SNPs in the SPOCK1 gene are associated with age at menarche. rs1859345 replicated across all groups studied (p < 10e-3), with the minor (C) allele associated with a (slightly) earlier age at menarche.
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[GWAS:Bone mineral density (spine)]
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rs6996321 significantly related to spine bone mineral density (p=0.002) and rs10914367 associated with hip BMD (p=0.028). Non-vertebral fracture risk was significantly increased in carriers of 'A' allele of rs9900972 (OR=2.06, p=0.0187) Interferon regulatory factor 6 (IRF6) and fibroblast growth factor receptor 1 (FGFR1) contribute to human tooth agenesis. A genome-wide linkage scan for cleft lip and cleft palate identifies a novel locus on 8p11-23.
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rs2619112 and rs916055 are associated with high bone mineral density in pre-menopausal women but low BMD in post-menopausal women
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rs1999805 increases susceptibility to Bone mineral density variations, lower for carriers of the A allele [OMIM:BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 11; BMND11]
Frequency: 47.8%
References:1
References:1
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[GWAS:Bone mineral density]
Frequency: 47.8%
References:8
References:8
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rs11898505 increases susceptibility to Osteoporotic fractures for carriers of the G allele [PharmGKB:Non-Curated GWAS results: New sequence variants associated with bone mineral density. (Initial Sample Size: 6,865 individuals; Replication Sample Size: 8,510 individuals); (Region: 2p16.2; Reported Gene(s): SPTBN1; Risk Allele: rs11898505-G); (p-value= 0.000004).This variant is associated with Bone mineral density (spine).] [GWAS:Bone mineral density (spine)]
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Osteoporosis [GWAS:Bone mineral density (paediatric, upper limb)]
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Found no association between rs1871054 and susceptibility to knee osteoarthritis.
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[GWAS:Bone mineral density]
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[GWAS:Bone mineral density]
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rs2152750 is in linkage disequilibrium with a polymorphism that increases susceptibility to Bone mineral density variations, lower for carriers of the A allele
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[GWAS:Bone mineral density]
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[GWAS:Bone mineral density (spine)]
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related IGF2R Ex16+88G>A rs998075 alters methylation affecting osteosarcoma
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[GWAS:Bone mineral density (hip)]
Frequency: 53.1%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: New sequence variants associated with bone mineral density. (Initial Sample Size: 6,865 individuals; Replication Sample Size: 8,510 individuals); (Region: 3p22.1; Reported Gene(s): NR; Risk Allele: rs10490823-G); (p-value= 0.000009).This variant is associated with Bone mineral density (hip).] [GWAS:Bone mineral density (hip)]
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Authors of this study of just 189 subjects conclude that rs3740199 polymorphism may affect occurrence of knee osteoarthritis and its progression (p = 0.018), and even speculate that this SNP's effect is 'remarkably gender-dependent and anatomical site-specific'. Of course, another alternative is that it's just another case of overinterpretation based on having too few samples for a properly powered SNP study. Only time will tell. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
Frequency: 55.4%
References:1
References:1
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Replication study of candidate genes/loci associated with osteoporosis based on genome-wide screening. [GWAS:Bone mineral density]
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Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study. [GWAS:Bone mineral density]
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rs7935346 increases susceptibility to Osteoporotic fractures for carriers of the G allele
Frequency: 58.4%
References:3
References:3
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[GWAS:MPV]
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avascular necrosis (AVN), a bone disease that produces osteonecrosis of the femoral head. The minor allele (C) frequency of rs2267439 showed a significant protective effect, while rs1052717 and rs2267443 were significantly associated with AVN risk
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[PharmGKB:Non-Curated GWAS results: New sequence variants associated with bone mineral density. (Initial Sample Size: 6,865 individuals; Replication Sample Size: 8,510 individuals); (Region: Xq21.2; Reported Gene(s): NR; Risk Allele: rs2710057-T); (p-value= 0.000001).This variant is associated with Bone mineral density (hip).] [GWAS:Bone mineral density (hip)]
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rs1559874 is in linkage disequilibrium with a polymorphism that increases susceptibility to Bone mineral density variations, lower for carriers of the G allele rs1559874 is in linkage disequilibrium with a polymorphism that increases susceptibility to Osteoporotic fractures 1.09 times for carriers of the G allele
Frequency: 64.6%
References:2
References:2
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[GWAS:Bone mineral density (hip)]
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[GWAS:Bone mineral density (hip)]
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Replication study of candidate genes/loci associated with osteoporosis based on genome-wide screening. [PharmGKB:Non-Curated GWAS results: New sequence variants associated with bone mineral density. (Initial Sample Size: 6,865 individuals; Replication Sample Size: 8,510 individuals); (Region: 11p11.2; Reported Gene(s): LRP4; Risk Allele: rs1007738-A); (p-value= 0.0000007).This variant is associated with Bone mineral density (hip).] [GWAS:Bone mineral density (hip)]
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A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. Replication study of candidate genes/loci associated with osteoporosis based on genome-wide screening. [GWAS:Bone mineral density]
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[OMIM:?] [GWAS:Bone mineral density (spine)]
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[OMIM:?] [GWAS:Bone mineral density (hip)]
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[GWAS:Bone mineral density]
Frequency: 70.8%
References:2
References:2
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[GWAS:Bone mineral density]
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rs6696981 increases susceptibility to Bone mineral density variations, lower for carriers of the G allele rs6696981 increases susceptibility to Osteoporotic fractures for carriers of the G allele [PharmGKB:Non-Curated GWAS results: New sequence variants associated with bone mineral density. (Initial Sample Size: 6,865 individuals; Replication Sample Size: 8,510 individuals); (Region: 1p36.12; Reported Gene(s): Intergenic; Risk Allele: rs6696981-G); (p-value= 0.00000002).This variant is associated with Bone mineral density (spine).] [GWAS:Bone mineral density (spine)]
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[GWAS:Bone mineral density]
Frequency: 77.9%
References:1
References:1
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[GWAS:Bone mineral density]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association with bone mass and geometry in the Framingham Heart Study (Initial Sample Size: 1,141 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Bone mineral density.] [GWAS:Bone mineral density]
Frequency: 78.8%
References:2
References:2
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rs10498760 is in linkage disequilibrium with a polymorphism that increases susceptibility to Bone mineral density variations, lower for carriers of the C allele
Frequency: 86.7%
References:1
References:1
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[GWAS:Bone mineral density]
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An osteopontin (SPP1) polymorphism is associated with systemic lupus erythematosus. Osteopontin and systemic lupus erythematosus association: a probable gene-gender interaction. Elevated plasma osteopontin level is associated with pelvic inflammatory disease.
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[GWAS:Bone mineral density]
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[OMIM:?] [GWAS:Bone mineral density (hip)]
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[OMIM:?] [GWAS:Bone mineral density (spine)]
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rs7740686 is in linkage disequilibrium with a polymorphism that increases susceptibility to Bone mineral density variations, lower for carriers of the T allele
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SNP rs235754, a variant located in the 3' region of the bone morphogenic protein-2 BMP2, has been reported to be associated with two parameters associated with bone density and thus the likelihood of bone fractures or osteoporosis. A study of Swedish women of varying ages found that rs235754 was significantly associated with the ultrasound parameters speed of sound and stiffness.
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
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rs3130340 increases susceptibility to Bone mineral density variations, lower for carriers of the T allele rs3130340 increases susceptibility to Osteoporotic fractures for carriers of the T allele [PharmGKB:Non-Curated GWAS Results: Multiple Genetic Loci for Bone Mineral Density and Fractures (Initial Sample Size: 5,861 individuals; Replication Sample Size: 7,925 individuals; Risk Allele: rs3130340-T). This variant is associated with Bone mineral density (spine).] [GWAS:Bone mineral density (spine)]
common in complete genomics
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rs7524102 increases susceptibility to Bone mineral density variations, lower for carriers of the A allele rs7524102 increases susceptibility to Osteoporotic fractures 1.12 times for carriers of the A allele Common variants in the region around Osterix are associated with bone mineral density and growth in childhood. Replication study of candidate genes/loci associated with osteoporosis based on genome-wide screening. OPG and RANK polymorphisms are both associated with cortical bone mineral density: findings from a metaanalysis of the Avon longitudinal study of parents and children and gothenburg osteoporosis and obesity determinants cohorts. Analysis of recently identified osteoporosis susceptibility genes in Han Chinese women. [PharmGKB:Non-Curated GWAS results: New sequence variants ass...
common in complete genomics
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rs6426748 is in linkage disequilibrium with a polymorphism that increases susceptibility to Bone mineral density variations, lower for carriers of the C allele rs6426748 is in linkage disequilibrium with a polymorphism that increases susceptibility to Osteoporotic fractures 1.15 times for carriers of the C allele
normal
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rs3736228 is a SNP in the LRP5 gene that is also known as Ala1330Val or A1330V; the more common (C) allele encodes the Ala (alanine), while the rarer (T) allele encodes the Val (valine), which is the risk allele. rs3736228(T) is associated with vertebral fractures and reduced bone mineral density (BMD), with an overall odds ratio for fractures of 1.06 per allele (CI: 1.01-1.12; 7802 fractures among 31,199 individuals studied). More specifically, the rs3736228(T) allele was associated with reduced lumbar spine BMD (p = 2.6 x 10<sup>-9</sup>), and femoral neck BMD (p = 5.0 x 10<sup>-6</sup>). Note that rs4988321, another LRP5 SNP (also known as Val667Met), was independently associated with BMD in this same study. news rs3736228 was associated with a 30% increase in th...
Magnitude: 0
Frequency: 75.2%
References:1
Frequency: 75.2%
References:1
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rs11121179 (p = 0.000005 for lumbar spine low bone mineral density, one of the major risk factor for osteoporosis)
common in complete genomics
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rs4140564, a SNP on chromosome 1 near the PTGS2 and PLA2G4A genes, has been associated with knee osteoarthritis. A study of 255 British patients, replicated subsequently in ~2,000 UK, Dutch and US patients, found that rs4140564 was associated with knee osteoarthritis in all populations studied with an overall odds ratio = 1.55, CI: 1.30-1.85, p < 6.9 x 10e-7. [PharmGKB:Curated GWAS results: Genome-wide Association Scan Identifies a Prostaglandin-Endoperoxide Synthase 2 Variant Involved in Risk of Knee Osteoarthritis (Initial Sample Size: 357 cases, 285 controls; Replication Sample Size: 1,177 cases, 2,372 controls). This variant is associated with Knee osteoarthritis.] [GWAS:Knee osteoarthritis]
Magnitude: 0
Frequency: 92.9%
Repute:Good
References:1
Frequency: 92.9%
Repute:Good
References:1
common in complete genomics
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The research paper suggests that the 3 snps rs17703883, rs12594287 and rs16964201 affect bone mineral density in men.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:4
Frequency: 100.0%
Repute:Good
References:4
common in complete genomics
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[PharmGKB:Curated GWAS results: Genome-wide Association and Follow-Up Replication Studies Identified ADAMTS18 and TGFBR3 as Bone Mass Candidate Genes in Different Ethnic Groups. (Initial Sample Size: 1,000 white individuals; Replication Sample Size: 4,925 white individuals, 350 Chinese hip fracture cases, 350 Chinese controls, 2,955 Chinese individuals, 908 West African men); (Region: 1p22.2; Reported Gene(s): TGFBR3; Risk Allele: rs17131547-A); (p-value= 0.000001).This variant is associated with Bone mineral density.] [OMIM:BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 14; BMND14] [GWAS:Bone mineral density]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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rs7775 (R324G) osteoarthritis at multiple joints (p = 0.07), particularly in the hip in women associated with osteoarthritis of the hip in females This is an arg324-to-gly (R324G) substitution Meta-analysis of 14 studies did not support a significant association between rs7775 and osteoarthritis. Functional variants within the secreted frizzled-related protein 3 gene are associated with hip osteoarthritis in females. Genetic variation in candidate osteoporosis genes, bone mineral density, and fracture risk: the study of osteoporotic fractures. No association of the polymorphisms of the frizzled-related protein gene with peak bone mineral density in Chinese nuclear families. Variant alleles of the Wnt antagonist FRZB are determinants of hip shape and modify the relationship between hip shap...
97 snps
(hide) Otitis
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
normal risk
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rs1800750, a SNP located at position -376 of the TNF gene, has been linked to increased risk for recurrent acute otitis in a study of 348 children. The (adjusted) odds ratio is 3.06 for (G;G) genotypes (p=0.07).
complex; generally normal risk
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rs361525 is also known as the TNF-238 SNP, and occasionally the rs361525(A) allele is referred to as 238.2 (with the more common (G) allele being 238.1). This SNP in the tumor necrosis factor-alpha gene has been linked to a wide variety of conditions: * Breast cancer ** A large study of over 5,000 Caucasian women found that rs361525(A) allele carriers were at somewhat elevated risk for breast cancer compared to the (G;G) genotype, with an odds ratio per allele of 1.18, CI: 1.04-1.35, p(trend)= 0.008. ** However, a 2009 European study of 30,000 breast cancer cases, compared to 30,000 controls, found no association, or as they put it, 'persuasive evidence against an overall association between invasive breast cancer risk and (this SNP)'. * Graft versus host disease (GVHD) ** A study of ~100 ...
3 snps
(hide) Otosclerosis
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rs17563(G) allele, coding for the amino acid alanine, confers susceptibility to otosclerosis (combined populations: p = 0.002; OR = 1.209; 95% CI: 1.070-1.370) [GWAS:Primary tooth development (time to first tooth eruption)]
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rs3178250(C;C)protected against otosclerosis (combined populations: p = 2.2 x 10(-4); OR = 2.027; 95% CI = 1.380-2.979
Normal otosclerosis risk
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Each C allele at rs3914132 decreases the likelihood of developing otosclerosis, which can cause hearing loss. [PharmGKB:Non-Curated In a GWAS done in Belgian-Dutch cases and controls (694 of each, split into a discovery and a replication set) and then in a second replication set of 455 French cases and 480 controls, rs3914132 was found to be associated with otosclerosis.] [OMIM:OTOSCLEROSIS; OTSC1] [GWAS:Otosclerosis]
3 snps
(hide) Ovarian cancer
higher risk of of coronary heart disease coronary heart disease
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rs662, also known as Q192R, is a SNP in the PON1 gene. It codes for amino acid 192 of the paraoxonase (PON) protein. Variants of this SNP affect PON catalytic efficiency and are correlated with Heart disease and trait-anxiety scores. The normal form, rs662(A), encodes a glutamine (Q), while the variant, rs662(G)), encodes an arginine (R). . While some populations show an association between this SNP and Heart disease, not all do. Perhaps the most striking finding was reported in Japanese patients with non-insulin dependent diabetes mellitus (NIDDM). NIDDM patients with either one or two rs662(G) alleles had a 9 fold higher risk of coronary heart disease compared with rs662(A;A) NIDDM patients. table of odds for cardiovascular disease outcomes 274 ovarian epithelial carcinoma cases and 452 ...
1.2x increased risk for ovarian cancer
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rs2072590 is a SNP on chromosome 2q31, in a noncoding region ~5 kb distal to the HOXD3 gene and ~10 kb proximal to HOXD1. A genome-wide association study ultimately including over 10,000 ovarian cancer patients found statistically strong (p = 3.8 × 10e?14) evidence for slightly elevated risk associated with the rs2072590(T) allele, with an odds ratio of 1.20 (CI: 1.14–1.25) as calculated for the serous subtype (of ovarian cancer), though it was significant for the other subtypes as well. [GWAS:None]
Frequency: 17.2%
References:0
References:0
normal risk?
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rs17647532 is a SNP in the GALNT1 gene that has a variant rarely seen in ovarian cancer, which may indicate it is a protective genotype. In a study of 829 patients, the rs17647532(C;C) homozygous genotype was calculated to have an odds ratio for developing ovarian cancer of 0.07 (CI: 0.01-0.53, p=0.00017). Unfortunately, perhaps, a subsequent (larger) study by the same authors using 6,965 cases and 8,377 controls from 14 studies forming the Ovarian Cancer Association Consortium was not able to find any significant association between this SNP and risk for (or from) ovarian cancer. As the authors state, 'this study underscores the need for replication of putative findings in genetic association studies'.
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Modifies risk of ovarian cancer in BRCA1 mutation carriers, study size 23,463 mutation carriers . [GWAS:Ovarian cancer]
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In a study conducted on 6,580 Nondiabetic Finnish Men, rs757210 in HNF1B gene showed nominal or significant associations with several lipoprotein traits. [GWAS:Ovarian cancer]
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rs4954956 was associated with increased ovarian cancer risk, particularly for serous ovarian cancer. The per minor allele odds ratio was 1.07 (CI: 1.01-1.13, P-trend=0.02) for all types of ovarian cancer and 1.14 (CI: 1.07-1.22, P-trend=0.00017) for serous ovarian cancer in this study of 2927 invasive ovarian cancer cases and 4143 controls from six ovarian cancer case-control studies. [OMIM:?]
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rs749292(A) associated with ovarian cancer risk in a codominant model for all races combined [AG versus AA genotype: odds ratio (OR), 1.48 and 95% confidence interval (CI), 1.07-2.04); GG versus AA: OR, 1.87 (CI, 1.24-2.82); Ptrend =0.002]. endometrial cancer *rs749292(A) allele OR of 1.14, 95% confidence interval of 1.09-1.21, and P = 7.1 x 10(-7) *rs727479(A) odds ratio per allele of 1.08, 95% confidence interval of 1.02-1.14, and P = 0.009 [OMIM:CYTOCHROME P450, FAMILY 19, SUBFAMILY A, POLYPEPTIDE 1; CYP19A1]
0.8x decreased risk for ovarian cancer
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rs3814113 is a SNP ~44kb upstream of the BNC2 gene on chromosome 9. A very large study of multiple populations, ultimately totaling almost 10,000 ovarian cancer patients and an equal number of matched controls, concluded that the per allele odds ratio associated with the rs3814113(C) allele was 0.79 (CI: 0.75-0.84, p=2.5x10e-17). This association held in 5 types of (ethnic) populations studied, and was strongest in association with serous ovarian cancers. An independent study of 10,000+ BRCA1 mutation carriers and almost 6,000 BRCA2 mutation carriers provided confirmation for the original report, finding the rs3814113(C) allele to be associated with a reduced risk of ovarian cancer among BRCA1 mutation carriers (per-allele hazard ratio 0.78, CI: 0.72 - 0.85, p = 4.8 × 10e-9) and BRCA2...
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The observed association of rs7797466 with ovarian cancer warrants confirmation in an independent study . *rs7797466 PMS2 rs7797466 may have a role in development of ovarian cancer
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cancer-genetics these snps influence genetic risk for prostate cancer rs2660753 showed a per-allele OR, 1.08 (95% confidence interval, 1.00-1.16; P = 0.06) An initial report of an association with between this SNP and risk for ovarian cancer was not replicated when the same authors expanded the study over 12 studies comprising 4,482 cases (and over 6,000 controls). [GWAS:Prostate cancer]
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A study population including a total of 5,206 invasive ovarian cancer cases (2,829 of which were serous) and 8,790 controls found an association between rs2287498 and serous invasive cancer (median per allele odds ratio 1.30, CI: 1.07-1.57).
Frequency: 82.3%
References:11
References:11
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rs17887200 and rs12951053 associated with ER negative breast cancer tumors (1.48 (1.11-1.93) p-trend = 0.01 and 1.29 (1.06-1.58) p-trend = 0.009, respectively) A study population including a total of 5,206 invasive ovarian cancer cases (2,829 of which were serous) and 8,790 controls found an association between rs12951053 and serous invasive cancer (median per allele odds ratio 1.19, CI: 1.01-1.38).
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Part of a haplotype Gs286, standalone effect for endometrial cancer and ovarian cancer is ambiguous. ''p''-values account for ethnic heterogenity of study population. Clarifying the PROGINS allele association in ovarian and breast cancer risk: a haplotype-based analysis [GWAS:Endometrial cancer]
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This SNP is associated with risk of breast cancer. MAST3: a novel IBD risk factor that modulates TLR4 signaling. Mutation screening of the MERIT40 gene encoding a novel BRCA1 and RAP80 interacting protein in breast cancer families. Common breast cancer susceptibility loci are associated with triple-negative breast cancer. Common variants at the 19p13.1 and ZNF365 loci are associated with ER subtypes of breast cancer and ovarian cancer risk in BRCA1 and BRCA2 mutation carriers. [GWAS:None]
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rs4151620(C;G) and rs4151620(G;G) are associated with a reduced risk of ovarian cancer compared with rs4151620(G;G) individuals. This snp has been linked to ovarian cancer Intron 17 of RB1 contains the open reading frame for the P2RY5 gene, and rs4151620 is perfectly correlated with rs2227311, which is located in the 5'-untranslated region of P2RY5 and is predicted to affect P2RY5 transcription. rs2854344 has been reported previously to be associated with breast cancer risk
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Two SNPs in block 4 were associated with an increased risk of ovarian cancer among homozygous carriers as compared with noncarriers: rs1042838 (PROGINS allele; odds ratio [OR] = 3.23, 95% confidence interval [CI] = 1.19 to 8.75, P = .022) and rs608995 (minor allele; OR = 3.10, 95% CI = 1.63 to 5.89, P<.001) Progesterone receptor variation and risk of ovarian cancer is limited to the invasive endometrioid subtype: results from the Ovarian Cancer Association Consortium pooled analysis.
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Based on a study of ~2500 female patients of European ancestry with sporadic postmenopausal breast cancer, this SNP in the FGFR2 showed the greatest risk. The risk allele is rs1219648(G), with a pooled odds ratio of 1.64 (CI:1.42-1.90) for rs1219648(G;G) homozygotes, and an odds ratio of 1.20 (CI: 1.07-1.42) for rs1219648(A;G) heterozygotes, compared with rs1219648(A;A) homozygotes. rs1219648 represents the SNP in the FGFR2 gene with the strongest association with breast cancer. However, nearby SNPs are almost as predictive. In particular, the following SNP alleles all have linkage values of 0.96 or greater with the rs1219648(G) allele in European populations: *rs2981579(A) *rs2420946(T) *rs11200014(A) An experimental rationale is presented indicating that this SNP is part of a haplotype t...
normal risk
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rs3731239 shows a slight protective association against breast cancer in a British study involving ~2300 patients. The odds ratio for the (C;C) vs (T;T) homozygotes is 0.90 (CI: 0.79-1.03, p=0.013). ovarian cancer rs3731239 rs602652 rs3212879 rs649392 rs3212891 rs2069391, rs2069414 rs17528736 rs3218036
normal
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rs4320932 is a SNP in the IF2 insulin-like growth factor 2 gene. A study totaling ~5,000 non-Hispanic white patients with ovarian cancer found a 13% decreased risk of ovarian cancer per copy of the rs4320932(G) allele carried (CI: 0.81-0.93, P-trend=7.4 × 10e-5). Associated with schizophrenia in a study of Croatians. Due to the limited number (~100 patients) and diversity of the studied population, more study is needed to confirm any link. The G allele was associated with an increased risk of schizophrenia with P < 0.001. Small size study with 212 cases linked the G allele earlier found protective against ovarian cancer increasing relapse by 3.05 (95% confidence interval CI: 1.47–6.37, P-trend 2*10e-4) and mortality 3.28 (95% CI: 1.64–6.57, P-trend 6*10e-5). Association...
normal risk
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Minor allele (T) of this SNP uniquely identifies what is known as the PROGINS allele in the progresterone receptor gene PGR. Two SNP's tagging a partial haplotype of the PGR gene were associated with an increased risk of ovarian cancer among homozygous carriers as compared with noncarriers: rs1042838 (PROGINS allele; odds ratio [OR] = 3.23, 95% confidence interval [CI] = 1.19 to 8.75, P = .022) and rs608995 (minor allele; OR = 3.10, 95% CI = 1.63 to 5.89, P<.001). The study suggest the effect is likely entirely due to rs608995, whose minor allele was almost always seen with PROGINS allele. For rs1042838, the risk allele in orientation to the corresponding dbSNP entry is (T). Subsequent studies have not replicated this high odds ratio, nor the apparent recessive model in this study. The ...
common
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rs2295190 is a SNP in the spectrin repeat containing, nuclear envelope 1 SYNE1 gene, located 19kb downstream of the estrogen receptor alpha ESR1 gene. A large study (over 5,000 cases) of ovarian cancer samples from the Ovarian Cancer Association Consortium concluded that carriers of a rs2295190(T) allele are at slightly increased risk for ovarian cancer (odds ratio 1.09, CI: 1.02-1.17, p=0.017).
Magnitude: 0
Frequency: 75.9%
References:7
Frequency: 75.9%
References:7
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rs10088218 is a SNP on chromosome 8q24, >700 kb distal to the CMYC gene in an area termed a 'gene desert'. A genome-wide association study ultimately including over 10,000 ovarian cancer patients found statistically strong (p = 8 × 10e-15) evidence for slightly reduced risk associated with the rs10088218(A) allele, with an odds ratio of 0.76 (CI: 0.7 – 0.81) as calculated for the serous subtype (of ovarian cancer). A large study of over 18,000 patients with epithelial ovarian cancer, including BRCA1 and BRCA2 carriers and a meta-analysis, has also found similar levels of decreased risk for the rs10088218(A) allele. [GWAS:None]
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This SNP has been linked to another SNP, rs4151620 which has been linked to ovarian cancer . More specifically: rs2227311(C) alleles were found to be perfectly correlated to rs4151620(G) alleles, and carriers of two rs4151620(G) alleles have a 5X reduced risk of developing ovarian cancer compared to carriers of two rs4151620(C) alleles, in a survey of ~5,000 women from the US, UK, and Denmark.
Magnitude: 0
Frequency: 78.4%
Repute:Good
References:1
Frequency: 78.4%
Repute:Good
References:1
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[GWAS:Ovarian cancer]
common in complete genomics
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rs2665390 is a SNP in chromosomal region 3q25, in the TCDD-inducible poly(ADP-ribose) polymerase TIPARP gene. A genome-wide association study ultimately including over 10,000 ovarian cancer patients found statistically strong (p = 7.1 × 10e-8) evidence for slightly elevated risk associated with the rs2665390(C) allele, with an odds ratio of 1.24 (CI: 1.15–1.34) as calculated for the serous subtype (of ovarian cancer). [GWAS:Ovarian cancer in BRCA1 mutation carriers]
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associated with breast cancer risk and ovarian cancer More specifically: carriers of two rs2854344(A) alleles have a 25% reduced risk of developing ovarian cancer compared to carriers of two rs2854344(G) alleles, in a survey of ~5,000 women from the US, UK, and Denmark. showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer
common/normal
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rs7651446 is a SNP within the TCDD-inducible poly(ADP-ribose) polymerase TIPARP gene on chromosome 3. Although not the first report, the first large validation associating the rs7651446(T) allele with increased risk for epithelial ovarian cancer came from a study of 18,174 individuals from 43 studies from the Ovarian Cancer Association Consortium. Subsequently, another study of over 18,000 patients, including BRCA1 and BRCA2 carriers as well as a meta-analysis, validated this association as the strongest (in terms of increasing risk) of a total of 18 known risk loci. The rs7651466(T) allele was reported as having a hazard ratio of between 1.50 - 1.94, depending on genetic background, with p values 10e-8 or lower. [GWAS:Ovarian cancer]
normal
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rs4986852 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 1040. The more common rs4986852(G) allele encodes Ser, while the rare rs4986852(A) allele encodes Asn; this variation is also known as Ser1040Asn or S1040N. A well known study published in 1994 looked at 10 family pedigrees with breast cancer and ovarian cancer susceptibility, including 63 breast cancer patients, and discovered what they believed were seven putative disease-causing mutations. rs4986852 was one of these variants. * See also Omim 113705.0011 [OMIM:?]
normal
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rs41293463 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 841. The more common rs41293463(C) allele encodes Arg, while the rare rs41293463(T) allele encodes Trp; this SNP is also known as R841W. A 1996 study of 305 cases in Southern California of breast cancer and ovarian cancer found 3 cases carrying the rs1800709(T) allele. In all three cases, there was a strong family history of breast, ovarian, or other cancers, and family members showed a high concordance of cancer incidence with the presence of this SNP. However, the age of cancer onset was the same as for sporadic cases. The authors conclude that this SNP may explain around 1% (CI: 0-1.7%) of all breast and ovarian cancers, at least for this population. Note: this SNP is rather unlikely to ...
normal
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The rs2740574(G) allele encodes a variant form of CYP3A4 known as CYP3A4*1B. rs2740574(G) alleles are associated with an ~10 fold higher risk of aggressive prostate cancer in African American males. [PMID 16414488, OMIM A pooled study (1,400+ samples) along with a replication study conducted by members of the Ovarian Cancer Association Consortium found a 2.5-2.8x increased risk for ovarian cancer] for rs2740574(G;G) individuals (CI: 1.2-6.5, p=0.017). The authors note that CYP3A4 encodes a key enzyme in estrogen metabolism and which may be linked to ovarian carcinogenesis. [PharmGKB:Curated Risk or phenotype-associated allele: CYP3A4*1B, rs2740574 G allele. Phenotype: CYP3A4*1B (rs2740574 G) allele carriers show a significantly increased risk for SCLC (OR = 2.25, p = 0.02), which showed a...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28897672 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 61. The more common rs28897672(T) allele encodes Cys, while the rare rs28897672(G) allele encodes Gly; this variation is also known as Cys61Gly or C61G. A study of 66 Polish families affected with breast cancer or ovarian cancer, often diagnosed at a relatively young age (< 50 years old), screened for BRCA1 mutations by sequencing. The C61G mutation accounted for 20% of the identified mutations in this group of families. * See also Omim 113705.0002 * Also represented as i5010326 by 23andMe [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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This SNP is often associated with ovarian cancer in Icelandic women, according to DeCode, however it appears to only due to linkage disequilibrium, the causitive mutation is a more rare indel which does not (yet) have an rs# assigned. [GWAS:Ovarian cancer]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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rs41293455 is a SNP causing an amino acid change in the breast cancer 1 BRCA1 gene at amino position 1443. The more common rs41293455(C) allele encodes Arg, while the rare rs41293455(T) allele encodes a stop codon. Another variant, rs41293455(G), encodes a Gly. A well known study published in 1994 looked at 50 family pedigrees with breast cancer and ovarian cancer susceptibility, discovering what they believed were eight putative disease-causing mutations (four frameshifts, two nonsense mutations) and an additional two missense mutations. rs41293455 was one of these variants. * See also Omim 113705.0016 * See also Omim 113705.0017 [OMIM:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs41293497 is a BRCA2 gene variant, with at least two variant alleles: C>G and C>A. [The C>T variant is also possible, however it is a synonymous change that is considered benign.] Alternative names for the pathogenic alleles include Tyr1894Ter, Y1894X, 5910C>G, and 5910C>A. Both the C>G and C>A variants are listed as causal breast cancer mutations in UMD, and as pathogenic by most submitters to ClinVar. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. In addition to presenting rs41293497, 23andMe has an additional C>G SNP at this position known as i5009383 on some of its microarrays.
Magnitude: 0
Repute:Good
References:13
Repute:Good
References:13
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Contrary to the claims of a test being marketed, a large study (8,500+ patients and >10,000 controls) found no evidence for any association between rs61764370 and any form of ovarian cancer. This letter in the Lancet challenges the claims of an association with triple-negative breast cancer in
common in clinvar
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rs523349 is a SNP in the steroid-5-alpha-reductase SRD5A2 gene; it is also known as V89L. In a study of a total of 1,466 Caucasian cases of ovarian cancer, the rs523349(G) allele showed a significant trend of increasing risk of ovarian cancer per rare allele (p = 0.00002). showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer
normal
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(C;C) predisposes to papillary thyroid carcinoma. Among 42 patients with familial breast cancer and 82 patients with ovarian cancer, those with at least one rs2910164(C) SNP tended to have been diagnosed at an earlier age than those with only (G) alleles. For the breast cancer patients, the difference in median age was between 45 vs 56 (p = 0.029) and for ovarian cancer patients, 45 vs 50, (p = 0.014). (G;G) males were two-fold more susceptible to hepatocellular carcinoma (OR = 2.016, 95% CI = 1.056-3.848, P = 0.034) perhaps an ambiguous flip? [OMIM:MICRO RNA 146A; MIRN146A]
but the rare allele is protective
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rs1045485, also known as D302H, is a SNP in the caspase-8 CASP8 gene. Several large studies indicate that the (C) allele of this SNP, located in exon 10 of the CASP8 gene, may reduce the risk of breast cancer in a dose dependent manner. The odds ratio is 0.89 for (C;G) and 0.74 for (C;C) carriers. article cancergenetics A 4-SNP haplotype including rs1045485 was significantly associated with breast cancer in a large European study (3,000+ cases, 3,000+ controls), with a per allele odds ratio of 1.3 (CI:1.12-1.49). chronic lymphocytic leukemia rs2266690 rs17028658 rs4505265 rs1045485 rs2779251 rs3136687 showed '''no association''' with ovarian cancer risk 4,624 invasive epithelial ovarian cancer cases and 8,113 controls of white non-Hispanic origin ovarian cancer No association seen between ...
38 snps
(hide) Pachyonychia congenita Type I
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148041.0002 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148067.0006 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148041.0003 [OMIM:?]
normal
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This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148067.0010 [OMIM:?]
normal
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This SNP has been found in patients with pachyonychia congenita Type I, and the risk allele appears to be a causative mutation for this (dominant) disorder. See also: OMIM 148067.0005 [OMIM:?]
5 snps
(hide) Pancreatic cancer
Higher risk for number of cancers
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600+ Korean lung cancer patients were part of a study that concluded that the rs664143(T) allele, as oriented vis-a-vis dbSNP, located in the ATM gene and also known as IVS62+60G>A, was associated with increased risk, with an odds ratio of 1.68 (CI: 1.1-2.1, p<0.05). In a study of 119 American patients with potentially resectable pancreatic cancer, the rs664143(C) allele was associated with poorer overall survival (ie response) to combined gerncitabine radiation therapy. Also, as 1 of 3 SNPs its risk allele is associated with poorer overall survival for pancreatic cancer patients being treated with combined gerncitabine radiation therapy; median overall survival times of 31.0, 16.2, and 10.5 months were calculated for pancreatic cancer patients carrying < or = 1, 2, and 3 risk all...
blood type O
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=Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women. |OA=23andMe blog each copy rs505922(C) is associated with 1.2x risk of pancreatic cancer influences ABO blood group [PharmGKB:Non-Curated GWAS results: Common susceptibility allele are unlikely to contribute as strongly as the FV and ABO loci to VTE risk: results from a GWAS approach. (Initial Sample Size: 419 cases, 1,228 controls; Replication Sample Size: 1,757 cases, 1,480 controls); (Region: 9q34.2; Reported Gene(s): ABO; Risk Allele: rs505922-C); (p-value= 0.000000000000004).This variant is associated with Venous thromboembolism.] [OMIM:?] [GWAS:Venous thromboembolism]
slightly reduced risk (0.77x) for pancreatic cancer
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23andMe reports that the G allele of this SNP appears to lower the risk of pancreatic cancer. Genome-wide association study of pancreatic cancer in Japanese population. [OMIM:?] [GWAS:Pancreatic cancer]
~1.2x increased risk for several types of cancer
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rs401681 is a SNP in the CLPTM1-like CLPTM1 gene. The following studies span several types of cancer, and over 30,000 cases and 45,000 controls. deCODE press release reports rs401681 linked to basal cell carcinoma and many cancers for individuals with shorter telomeres, whereas those with long telomeres are at greater risk of melanoma. Neighboring rs2736098 also increases risk of cancer by affecting telomerase reverse transcriptase. The risk of these different cancers conferred by these two SNPs appears to be independent. 23andMe blog rs2736098 and rs401681 linked to many cancers, including susceptibility to pancreatic cancer However, a very large study (encompassing thousands of cases and controls) found no association between rs401681 and either (1) mean telomere length, or, (2) breast c...
poorer response to pancreatic cancer combined treatment
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rs2227928, also known as Ex4+340C>T or T211M, is a SNP in the ATR gene. Although not significant on it's own, as 1 of 3 SNPs its risk allele (rs2227928(C)) is associated with poorer overall survival for pancreatic cancer patients being treated with combined gerncitabine radiation therapy. Median overall survival times of 31.0, 16.2, and 10.5 months were calculated for pancreatic cancer patients carrying < or = 1, 2, and 3 risk alleles from rs664143(C), rs2227928(C), and rs521102(T;T), respectively (P=0.004).
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The C allele of this SNP is ssociated with slightly higher risk of pancreatic cancer. [OMIM:?] [GWAS:Pancreatic cancer]
Frequency: 53.1%
References:1
References:1
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[GWAS:Pancreatic cancer]
Frequency: 56.6%
References:1
References:1
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[GWAS:Pancreatic cancer]
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[GWAS:Type 2 diabetes]
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A 2014 study 'Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer' of 7,683 European cases and 14,397 controls found the minor allele rs7190458(A) in BCAR1 (breast cancer anti-estrogen resistance 1) conferring risk of statistically genome-wide significance (per-allele odds ratio (OR) = 1.46, 95% confidence interval (CI) 1.30-1.65, P = 1.1E-10) for Pancreatic cancer.
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The T allele of this SNP is associated with higher risk of pancreatic cancer. Phosphodiesterase 8B gene variants are associated with serum TSH levels and thyroid function. Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. Genetic variants associated with Von Willebrand factor levels in healthy men and women identified using the HumanCVD BeadChip. [PharmGKB:Non-Curated GWAS results: Population-based genome-wide association studies reveal six loci influencing plasma levels of live...
11 snps
(hide) Panic disorder
3.6x increased risk of sexual dysfunction when taking SSRI Antidepressants. Selective Seratonin Reuptake Inhibitors (citalopram (Celexa), escitalopram (Lexapro), fluoxetine (Prozac), paroxetine (Paxil), or sertraline (Zoloft)) cause worse sexual dysfunction (a common side-effect) in people with this SNP. Note that research has shown Saffron is effective at reversing the sexual dysfunction from SSRI anti-depressants.
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
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Polymorphisms in the serotonin receptor gene HTR2A are associated with quantitative traits in panic disorder. Association of genetic, psychological and behavioral factors with sleep bruxism in a Japanese population.
higher risk for RA
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rs6313, also known as T102C, is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6313(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs1328674 in dbSNP is opposite that cited by this publication; therefore, with respect to dbSNP, the haplotype of risk as cited above is CACC rather than CTCC. see also gs108 and gs226 Polymorphisms in the serotonin receptor gene HTR2A are associated with quantitative traits in panic disorder. [PharmGKB:Curated Risk or phenotype-associated allele (s): T/T. Phenotype: Patients, with a diagnosis of probable Alzheimer's disease, carryi...
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The haplotype A-A-G for SNPs rs3794808, rs140701 and rs4583306 has a 1.7x increased risk for panic disorder.
Normal risk for anxiety disorders
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A study of patients with panic disorder or social anxiety disorder, both moderately heritable anxiety disorders, concluded that the rs140701(A) allele was associated with increased risk for both disorders. This SNP was actually part of a tightly linked haplotype A-A-G (for SNPs rs3794808, rs140701 and rs4583306, respectively) that had 1.7x increased risk for panic disorder (CI: 1.2-2.3).
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 3p26.1; Reported Gene(s): GRM7; Risk Allele: rs3749380-?); (p-value= 0.000002).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 17q25.1; Reported Gene(s): SDK2; Risk Allele: rs3816995-?); (p-value= 0.0000002).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 1q32.1; Reported Gene(s): PKP1; Risk Allele: rs860554-?); (p-value= 0.00000005).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 14q23.1; Reported Gene(s): Intergenic; Risk Allele: rs4901869-?); (p-value= 0.000006).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 13q32.1; Reported Gene(s): Intergenic; Risk Allele: rs9302001-?); (p-value= 0.0000003).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
Frequency: 46.9%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 1p13.3; Reported Gene(s): Intergenic; Risk Allele: rs12061304-?); (p-value= 0.000001).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
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Polymorphisms in the serotonin receptor gene HTR2A are associated with quantitative traits in panic disorder.
Frequency: 64.6%
References:4
References:4
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 8p21.1; Reported Gene(s): CLU; Risk Allele: rs17466684-?); (p-value= 0.0000007).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
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Polymorphisms in the serotonin receptor gene HTR2A are associated with quantitative traits in panic disorder.
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 21q21.1; Reported Gene(s): USP25; Risk Allele: rs2823455-?); (p-value= 0.000009).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 12q24.33; Reported Gene(s): Intergenic; Risk Allele: rs7299940-?); (p-value= 0.000007).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 6q25.1; Reported Gene(s): PLEKHG1; Risk Allele: rs9372078-?); (p-value= 0.0000005).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 6p12.3; Reported Gene(s): TNFRSF21; Risk Allele: rs2103868-?); (p-value= 0.000005).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 5q21.1; Reported Gene(s): Intergenic; Risk Allele: rs4702982-?); (p-value= 0.000006).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 19q13.33; Reported Gene(s): Intergenic; Risk Allele: rs3810265-?); (p-value= 0.000004).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of panic disorder in the Japanese population. (Initial Sample Size: 200 Japanese cases, 200 Japanese controls; Replication Sample Size: NR); (Region: 12q13.13; Reported Gene(s): CALCOCO1; Risk Allele: rs941184-?); (p-value= 0.0000003).This variant is associated with Panic disorder.] [GWAS:Panic disorder]
21 snps
(hide) Parkinson disease 8
Frequency: 38.9%
References:5
References:5
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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First discovered in 2004, rs34637584 is a SNP indicating a position within the LRRK2 that encodes a variant protein. This SNP is commonly referred to as the G2019S variant (or, mutation) based on the potential change from glycine (encoded by rs34637584(G) allele) to serine (encoded by the rs34637584(A) allele) at position 2019 of the LRRK2 protein. One copy of a rs34637584(A) allele is sufficient to greatly increase one's risk for Parkinson's disease. It is considered a disease causing mutation because it is rarely found in healthy, elderly people without Parkinson's disease, and it has been found in both familial and sporadic types of the disease. While there are many different SNPs that can influence one's risk for Parkinson's disease, rs34637584 is an especially common cause of the dise...
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
normal
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In perfect contrast to another SNP also within the LRRK2 gene, rs34637584, this SNP, rs34778348, is not found in Caucasian populations but is found in Asian populations. A case-control study of 989 Chinese subjects concluded that the odds ratio for Parkinson's disease was 2.1 for rs34778348(A) carriers (CI: 1.1-3.9, p = 0.014). This SNP was estimated to account for 4% of all Parkinson cases in this population. 23andMe blog Parkinson's disease [OMIM:LEUCINE-RICH REPEAT KINASE 2; LRRK2] [GWAS:None]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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Multiple LRRK2 variants modulate risk of Parkinson disease: a Chinese multicenter study. [OMIM:LEUCINE-RICH REPEAT KINASE 2; LRRK2]
normal
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Also known as R1628P, rs33949390 is a SNP in the LRRK2 gene. A study of Chinese patients with Parkinson's disease concluded that in this population, after adjustments were made for age, age of onset, and gender, rs33949390(C) carriers were 3.3x more likely to develop the disease than noncarriers (CI: 1.4- 7.9, p = 0.007). [OMIM:LEUCINE-RICH REPEAT KINASE 2; LRRK2]
14 snps
(hide) Parkinson's disease
Magnitude: 1.5
Normal Parkinson's Disease Risk
The (G;G) genotype at this position is considered protective against Parkinson's Disease, but you don't have it. You instead have the more common rs10513789(T;T) which does not reduce your risk. see also gs249 for the more common heterozygote form http://www.genomicslawreport.com/index.php/2012/06/01/patenting-and-personal-genomics-23andme-receives-its-first-patent-and-plenty-of-questions/
Slightly increased risk of developing Parkinson's Disease
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[GWAS:Parkinson's disease]
Slightly increased risk of developing Parkinson's Disease
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rs9652490 is a SNP in the LINGO1 gene. Note: it is unclear why one set of authors report the risk allele for essential tremors to be (G), while the others just as clearly report the risk allele to be (A). A follow-up case-control study replicated the original association of rs9652490(A;A) to an ~2x increased risk for Parkinson's disease, but also found the same risk for essential tremor (ET), thus linking the two diseases. The ET study was based on ~300 patients. 23andMe blog 'In a combined analysis of 752 subjects with essential tremor from Iceland, Austria, Germany and the United States and 15,797 controls, Stefansson et al found that the G version of rs9652490 in the LINGO1 gene is associated with increased odds of the condition. Carrying one G increases the odds of essential tremor by ...
Slightly increased risk of developing Parkinson's Disease
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[OMIM:?] [GWAS:Parkinson's disease]
Slightly increased risk of developing Parkinson's Disease
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[GWAS:Parkinson's disease]
Magnitude: 1.25
Frequency: 55.8%
References:0
Frequency: 55.8%
References:0
Very common. Normal risk of Parkinson's disease. Approximately 55% of non-asian people have this genotype which is associated with slightly higher risk of Parkinson's disease when compared to genotype (G;G). It is notable because it is the first SNP patented by 23andMe rs10513789(T) increased risk of developing Parkinson's Disease GenomicsLawReport
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23andMe reports that the G allele of rs10513789 is associated with 0.8 times lower odds of Parkinson's disease. 23andMe has a patent covering this snp. http://blog.23andme.com/2012/05/28/announcing-23andmes-first-patent/ See also gs249 and gs248
slightly higher risk of developing Parkinson's Disease for caucasians but it has failed to reproduce in Greeks and Chinese populations. If there is an effect is is very small.
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People with two copies of the T allele at rs6812193 appear to have a slightly lower risk of Parkinson's disease. The same researchers identified another risk allele for Parkinson's disease at rs11868035. plos [GWAS:Parkinson's disease]
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[OMIM:?] [GWAS:None]
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'Dissection of the genetics of Parkinson's disease identifies an additional association 5′ of SNCA and multiple associated haplotypes at 17q21' suggests this is Parkinson's Disease associated together with rs356220, masked in other GWAS by rs2736990 via Simpson's paradox. Association replicated in French dataset with r^2 0.98 LD rs2301134 substituted.
Normal risk of developing Parkinson's Disease
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rs2736990 is a SNP associated with Parkinson’s disease (PD), a neurodegenerative disorder characterized by the degradation of dopamine-producing neurons in the substantia nigra. Rs273990 is located on chromosome 4q22 in the synuclein-alpha SNCA locus. The function of SNCA is not fully understood, but it predominately found in the presynaptic terminals of neurons, and it is thought that it plays a role in maintaining adequate supplies of synaptic vesicles. SNCA is also a major component of Lewy Bodies (LB), protein accumulations often found in neurons in patients with PD. The best evidence for the association of rs2736990 with PD was provided in a genome-wide association study (GWAS) that found an increased frequency of the minor C allele (T is the major allele) in position 90897564 a...
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defines the PARK10 locus; this SNP is reported to be associated with age of onset of Parkinson's disease
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[GWAS:Parkinson's disease]
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[GWAS:None]
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The (G) allele of this snp has been implicated in a somewhat increased risk of developing late onset Parkinson's disease
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Mentioned in the 23andMe Parkinson's disease patent along with rs10513789
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Aldehyde dehydrogenase variation enhances effect of pesticides associated with Parkinson's disease. 5 tagSNPs in ALDH2 (ie, rs737280, rs968529, rs16941667, rs16941669, and rs9971942) as well as rs671 (ie, ALDH2*2)
Frequency: 45.3%
References:1
References:1
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Four case-control series were combined along with previous GWAS results, yielding a 1.3x increased risk for Parkinson's disease among rs11155313 minor allele carriers.
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may influence Parkinson's disease abstract may influence brain structure [OMIM:GLYCOGEN SYNTHASE KINASE 3-BETA; GSK3B]
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Parkinson's disease The risk alleles for each SNP identified from conditional logistic regression, rs1721100 C, rs1721082 T and rs1799836 A, are consistent with previous reports. Significant interaction between this MAOB SNP and a FGF20 SNP, rs1721100 was also noticed.
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[GWAS:Parkinson's disease]
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[OMIM:?] [GWAS:Parkinson's disease]
Frequency: 57.5%
References:1
References:1
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[GWAS:Parkinson's disease]
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Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. [PharmGKB:Non-Curated GWAS results: Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data (Initial Sample Size: 267 cases, 270 controls; Replication Sample Size: NR). This variant is associated with Parkinson's disease.] [GWAS:Parkinson's disease]
Magnitude: 1
Frequency: 62.5%
Repute:Good
References:2
Frequency: 62.5%
Repute:Good
References:2
Normal risk of developing Parkinson's Disease
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Detecting disease-associated genotype patterns. Phactr2 and Parkinson's disease. [PharmGKB:Non-Curated GWAS results: Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data (Initial Sample Size: 267 cases, 270 controls; Replication Sample Size: NR). This variant is associated with Parkinson's disease.] [GWAS:Parkinson's disease]
Frequency: 73.5%
References:0
References:0
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Aldehyde dehydrogenase variation enhances effect of pesticides associated with Parkinson's disease. 5 tagSNPs in ALDH2 (ie, rs737280, rs968529, rs16941667, rs16941669, and rs9971942) as well as rs671 (ie, ALDH2*2)
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Originally reported to be one of 13 SNPs found in whole genome association study to be associated with Parkinson's disease. However, neither it (nor the other 13) appeared to be associated with Parkinson's disease in an independent study of 663 Caucasian patients. High-resolution whole-genome association study of Parkinson disease. Genomewide association, Parkinson disease, and PARK10. No evidence for association with Parkinson disease for 13 single-nucleotide polymorphisms identified by whole-genome association screening. A case-control association study of the 12 single-nucleotide polymorphisms implicated in Parkinson disease by a recent genome scan.
Normal risk of developing Parkinson's Disease
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rs2697962 is in linkage disequilibrium with a polymorphism that increases susceptibility to Parkinson's disease 1.67 times for carriers of the A allele
Frequency: 80.5%
References:1
References:1
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[GWAS:Parkinson's disease]
Frequency: 82.3%
References:0
References:0
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see gs248 patented by 23andMe to diagnose Parkinson's disease
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Mentioned in the 23andMe Parkinson's disease patent along with rs10513789
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[GWAS:Parkinson's disease]
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Aldehyde dehydrogenase variation enhances effect of pesticides associated with Parkinson's disease. 5 tagSNPs in ALDH2 (ie, rs737280, rs968529, rs16941667, rs16941669, and rs9971942) as well as rs671 (ie, ALDH2*2)
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rs6692804 was the only SNP found to be significantly (p = 0.03) associated with Parkinson's disease risk in a study of 525 patients.
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linked to late onset Parkinson's disease
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Parkinson's disease The risk alleles for each SNP identified from conditional logistic regression, rs1721100 C, rs1721082 T and rs1799836 A, are consistent with previous reports. Significant interaction between this FGF20 SNP and a MAOB gene SNP, rs1799836 was also noticed. [OMIM:FIBROBLAST GROWTH FACTOR 20; FGF20]
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Associated with Parkinson's disease based on a conditional logistic regression analysis. Variation in the miRNA-433 binding site of FGF20 confers risk for Parkinson disease by overexpression of alpha-synuclein.
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rs7702187 increases susceptibility to Parkinson's disease 1.74 times for carriers of the A allele rs7702187 had no association with the risk of developing Parkinson's disease in a study of 340 Han Chinese patients. [PharmGKB:Non-Curated GWAS results: High-resolution whole-genome association study of Parkinson disease (Initial Sample Size: 443 sib pairs; Replication Sample Size: 332 cases, 332 controls). This variant is associated with Parkinson's disease.] [OMIM:PARKINSON DISEASE; PD] [GWAS:Parkinson's disease]
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rs10200894 increases susceptibility to Parkinson's disease 1.84 times for carriers of the C allele
normal
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rs356219, a tagging SNP in the SNCA gene for a Parkinson's disease associated haplotype, predicts the amount of SNCA (alpha-synuclein) mRNA found in post mortem substantia nigra and cerebellum brain tissue. replicates the association of rs356219 with late-onset Parkinson's disease, calculating an odds ratio of 1.3 (CI: 1.13 - 1.5, p=2x10e-4) per rs356219(G) allele among the 1145 patients from northern Spain studied. Linkage disequilibrium patterns and tagSNP transferability among European populations. Tau and alpha-synuclein in susceptibility to, and dementia in, Parkinson's disease. Genetic variability in the SNCA gene influences alpha-synuclein levels in the blood and brain. Cerebellar alpha-synuclein levels are decreased in Parkinson's disease and do not correlate with SNCA polymorphism...
normal risk of parkinson's disease
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CC linked to parkinson's disease We provide evidence for a novel, strong and reproducible association of the PITX3 promoter SNP rs3758549 : C>T (p=0.004) with PD. The C-allele appears to be a recessive risk allele with an estimated population frequency of 83%.
Magnitude: 0
Frequency: 51.8%
References:5
Frequency: 51.8%
References:5
normal
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rs11868035 is one of several SNPs associated with the SREBF1 gene that show a modest association with type-2 diabetes. A study of ~2,000 Caucasian patients (and 10,000+ controls) led to an odds ratio of 1.19 (CI: 1.07-1.33, p=0.002) for the minor (risk) allele, rs11868035(A), in the orientation as in dbSNP. type-2 diabetes rs2297508(C) and rs11868035(C) This SNP rs11868035 and rs1057217 are associated with increased risk of schizophrenia in German and Scandinavian samples. This SNP and rs6812193 are reported to affect risk of Parkinson's disease. plos Polymorphisms in the gene encoding sterol regulatory element-binding factor-1c are associated with type 2 diabetes. [PharmGKB:Curated This SNP in the SREBF1 gene was strongly associated with schizophrenia in German, Danish and Norwegian samp...
common/normal Val/val (normal) variant of the Val66Met snp in the BDNF gene that codes for brain-derived neurotrophic factor. Met/met is associated with susceptibility to neuropsychiatric disorders.
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
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[PharmGKB:Non-Curated GWAS results: Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data (Initial Sample Size: 267 cases, 270 controls; Replication Sample Size: NR). This variant is associated with Parkinson's disease.] [GWAS:Parkinson's disease]
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rs1559085 is a SNP in the calpastatin CAST gene. A significant association (p = 0.0167) between Parkinson's disease and rs1559085 was found in an analysis of the Center for Inherited Disease Research's (CIDR) genome-wide association study in familial PD. Genomewide association study for susceptibility genes contributing to familial Parkinson disease.
Magnitude: 0
Frequency: 75.2%
Repute:Good
References:4
Frequency: 75.2%
Repute:Good
References:4
common on affy axiom data
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Genomewide association study for susceptibility genes contributing to familial Parkinson disease. A unified framework for multi-locus association analysis of both common and rare variants. [GWAS:Parkinson's disease]
common in complete genomics
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rs2313982 increases susceptibility to Parkinson's disease 2.01 times for carriers of the T allele
Magnitude: 0
Frequency: 84.1%
Repute:Good
References:3
Frequency: 84.1%
Repute:Good
References:3
common in complete genomics
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Aldehyde dehydrogenase variation enhances effect of pesticides associated with Parkinson's disease. 5 tagSNPs in ALDH2 (ie, rs737280, rs968529, rs16941667, rs16941669, and rs9971942) as well as rs671 (ie, ALDH2*2)
Magnitude: 0
Frequency: 84.5%
Repute:Good
References:0
Frequency: 84.5%
Repute:Good
References:0
common in complete genomics
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rs16851009 increases susceptibility to Parkinson's disease 1.84 times for carriers of the T allele Genomewide association, Parkinson disease, and PARK10. No evidence for association with Parkinson disease for 13 single-nucleotide polymorphisms identified by whole-genome association screening. A case-control association study of the 12 single-nucleotide polymorphisms implicated in Parkinson disease by a recent genome scan.
Magnitude: 0
Frequency: 84.8%
References:16
Frequency: 84.8%
References:16
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[OMIM:?] [GWAS:Parkinson's disease]
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:1
Frequency: 85.0%
Repute:Good
References:1
common in complete genomics
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Association of GWAS loci with PD in China. An association between the PARK16 locus and Parkinson's disease in a cohort from eastern China. [OMIM:?] [GWAS:Parkinson's disease]
normal
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SNP rs283413, also known as G78stop or Gly78X, encodes a rare variant of the ADH1C gene that leads to a truncated alcohol dehydrogenase protein. These types of proteins are involved in detoxification and may be linked to neurodegenerative diseases. The rs283413(G) allele is the more common, encoding the amino acid glycine (Gly); the quite rare rs283413(T) allele encodes the variant stop codon (X). Originally identified in three Swedish patients with Parkinson's disease (PD), a study of ~1000 PD patients vs. ~1000 controls indicated an odds ratio for the risk allele of 3.25 (CI:1.31-8.05). [This risk is effectively for heterozygotes, since the risk allele is so rare that no homozygotes for it were observed.] In a study of 40 index cases, 10% were found to harbor the rs283413(T) risk allele....
normal
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i400415, also known as N370S (risk genotype CC) Possibly associated with Gaucher's disease. * Type I (N370S homozygote), the most common, also called the 'non-neuropathic' type occurs mainly in Ashkenazi Jews, at 100 times the occurrence in the general populace. The median age at diagnosis is 28 years of age, and life expectancy is mildly decreased. There are no neurological symptoms. rs76763715 Parkinson's disease Gaucher Disease
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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First discovered in 2004, rs34637584 is a SNP indicating a position within the LRRK2 that encodes a variant protein. This SNP is commonly referred to as the G2019S variant (or, mutation) based on the potential change from glycine (encoded by rs34637584(G) allele) to serine (encoded by the rs34637584(A) allele) at position 2019 of the LRRK2 protein. One copy of a rs34637584(A) allele is sufficient to greatly increase one's risk for Parkinson's disease. It is considered a disease causing mutation because it is rarely found in healthy, elderly people without Parkinson's disease, and it has been found in both familial and sporadic types of the disease. While there are many different SNPs that can influence one's risk for Parkinson's disease, rs34637584 is an especially common cause of the dise...
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
normal
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In perfect contrast to another SNP also within the LRRK2 gene, rs34637584, this SNP, rs34778348, is not found in Caucasian populations but is found in Asian populations. A case-control study of 989 Chinese subjects concluded that the odds ratio for Parkinson's disease was 2.1 for rs34778348(A) carriers (CI: 1.1-3.9, p = 0.014). This SNP was estimated to account for 4% of all Parkinson cases in this population. 23andMe blog Parkinson's disease [OMIM:LEUCINE-RICH REPEAT KINASE 2; LRRK2] [GWAS:None]
extensive metabolizer
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The normal (or wild type) form of this SNP is a (G). The (A) form disrupts proper mRNA formation, resulting in a nonfunctional CYP2D6 protein. The associated allele is also known as CYP2D6*4. The CYP2D6*4 allele is the most common nonfunctioning variant of CYP2D6. If two copies of this (or similar) changes are inherited, poor metabolism ('PM') of debrisoquine is observed. Many other drugs are typically first metabolized by CYP2D6 including dextromorphan, sparteine, metoprolol, nortriptyline and many other antidepressants and codeine. Of course, sometimes the active form of a drug is the one post-CYP2D6 metabolism; an example of this is tamoxifen, where the active form (endoxifen) is formed primarily via CYP2D6 metabolism; less functioning CYP2D6 can mean less benefit from taking the drug. ...
common in complete genomics
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rs35866326 increases susceptibility to Parkinson's disease 1.88 times for carriers of the C allele
normal
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Also known as R1628P, rs33949390 is a SNP in the LRRK2 gene. A study of Chinese patients with Parkinson's disease concluded that in this population, after adjustments were made for age, age of onset, and gender, rs33949390(C) carriers were 3.3x more likely to develop the disease than noncarriers (CI: 1.4- 7.9, p = 0.007). [OMIM:LEUCINE-RICH REPEAT KINASE 2; LRRK2]
1 genoset 61 snps
(hide) Pelvic organ prolapse
normal
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rs1800255 is a SNP in the alpha I chain of the type III collagen protein-encoding COL3A1 gene. A relatively small study (200 patients) reported an odds ratio of 5 (CI: 1.4-17.1) between rs1800255(A;A) homozygotes and risk for pelvic organ prolapse. No significance was found for the heterozygous genotype. [OMIM:?]
1 snp
(hide) Pendred Syndrome
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
common in clinvar
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rs111033199, also known as V138F, is a SNP in the SLC26A4 gene associated with the hearing loss condition known as Pendred Syndrome. [OMIM:?]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
common in clinvar
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rs111033244, also known as E384G, is a SNP in the SLC26A4 gene associated with the hearing loss condition known as Pendred Syndrome. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs121908362, also known as H723R, is a SNP in the SLC26A4 gene associated with the hearing loss condition known as Pendred Syndrome. [OMIM:?]
9 snps
(hide) Periodontitis
Increased risk of mental disorders
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rs16944 is a SNP in the interleukin 1, beta gene, a member of the cytokine family involved in the inflammatory response. The rs16944 G;G genotype is associated with risk for multiple mental illnesses. An increased risk for schizophrenia was found in a genetic association study of 2111 Caucasian individuals with an odds ratio of 1.24 (95% CI 1.09, 1.41) . Studies examining the brains of schizophrenic and bipolar individuals found reduced gray matter and hypoactivity associated with the G;G genotype. Additionally, this genotype is associated with impaired ability to achieve remission in a study of 256 Caucasian individuals with depression (odds ratio = 1.74; 95% confidence interval 1.2-4.3). The rs16944 A allele increases susceptibility to Osteoarthritis, with 1.80 times for heterozygotes (A...
1.3x increased coronary artery disease risk
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rs1333048 increases susceptibility to coronary artery disease 1.30 times for heterozygotes (AC) and 1.54 times for homozygotes (CC) rs1333048 2x risk for periodontitis and a confirmation of coronary heart disease 23andMe blog [OMIM:?]
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
1.6x increased risk for periodontitis
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rs1537415 is an intronic SNP in the glycosyltransferase 6 domain containing 1 GLT6D1 gene. In a combined study of 1,758 Dutch and German subjects, the rs1537415(G) allele was associated with increased risk for periodontitis, at an odds ratio of 1.59 (CI: 1.36-1.86, p=5.5x10e-9).
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rs3795391 (A > G) of the S100A8 gene might contribute to periodontitis susceptibility
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Associated with periodontitis in a study of Chinese patients. rs2228570 aka rs10735810 allele (A) observed for breast cancer odds ratio (OR) of 1.26 Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. Variants in the vitamin D receptor gene and asthma. Gene-environment interaction effects on the development of immune responses in the 1st year of life. Vitamin D receptor polymorphisms are associated with Graves' disease in German and Polish but not in Serbian patients. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Polymorphisms in the ...
Intermediate risk of low bone mineral density disorders
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rs1544410, also known as the BsmI polymorphism, is a SNP in the Vitamin D receptor (VDR). Multiple studies examining bone mineral density (BMD) in women have associated the A allele with increased risk of low BMD , , & . Additionally, A meta-analysis of 26 studies estimated a decreased risk of osteoporosis associated with the G;G genotype with an odds ratio of 0.61, 95% CI, 0.40-0.92 . rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
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[GWAS:Periodontitis]
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[GWAS:Periodontitis]
normal
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rs1143634, also known as +3954, is a SNP in the IL-1 beta IL1B gene. A study of 556 adults in the Western Australian coronary heart disease (CHD) population concluded that rs1143634(T;T) homozygotes had larger waist circumference, by 1.8cm on average, compared to major allele (C;C) homozygotes. This association was even more pronounced in patients with higher levels of obesity or inflammatory markers. rs1143634 increases susceptibility to Alopecia Areata 2.67 times for heterozygotes (CT) and 1.13 times for homozygotes (TT) rs1143634 increases susceptibility to Alzheimer's disease 2.33 times for homozygotes (TT) rs1143634 increases susceptibility to Cervical lesions, low-grade squamous intraepithelial lesions 4.29 times for heterozygotes (CT) and 3.57 times for homozygotes (TT) rs1143634 in...
Magnitude: 0
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13 snps
(hide) Peripheral arterial disease
1.8x increased risk of lung cancer; reduced response to alcohol, therefore possibly increased risk of alcohol abuse
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rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...
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rs7025486(A) was associated with up to a 20% increased risk of the various vascular diseases, with an odds ratio of 1.21 for abdominal aortic aneurysm (AAA) (p = 4.6x10-10), 1.18 for early onset myocardial infarction (MI) (p = 3.1x10-5), 1.14 for peripheral arterial disease PAD (p = 3.9x10-5), and 1.2 for pulmonary embolism (PE) (p = 00030), but it was not associated with intracranial aneurysm or ischemic stroke. An individual who carried two copies of this allele would have around a 44% increased risk of AAA. No association was seen between the A allele and common risk factors for arterial and venous disease—smoking, lipid levels, obesity, type 2 diabetes, and hypertension. theheart.org DeCode reports that the rs7025486(A;A) genotype is associated with 1.21x odds of peripheral arter...
2 snps
(hide) Peutz-Jeghers syndrome
common in clinvar
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rs59912467, also known as F354L or Phe354Leu, is a SNP in the STK11 gene on chromosome 19. One report links the minor allele of this SNP to Peutz-Jeghers syndrome (PJS), however, that report also mentions that the patient's mother was asymptomatic, and since PJS is usually inherited in a dominant manner, this implies quite variable penetrance. In ClinVar, this mutation is listed as of uncertain significance, since there are reports indicating it is benign as well as reports indicating it is pathogenic. See also OMIM 602216.0024 This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about.
1 snp
(hide) Phenylketonuria
References:0
common in clinvar
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rs5030858, also known as Arg408Trp or R408W, is a SNP in the phenylalanine hydroxylase PAH gene on chromosome 12. If present in two copies, or present along with another PAH mutant, this SNP is associated with phenylketonuria. A good write-up on this SNP can be found at OMIM. [OMIM:?]
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67 snps
(hide) Photic sneeze reflex
Frequency: 44.2%
References:1
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a suggestive photic sneeze reflex association with rs11856995 (score 7.13 and OR of 0.78)
Frequency: 46.9%
References:1
References:1
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For photic sneeze reflex, we find a novel association with rs10427255 (score 10.9 and an OR of 1.32). We also find a suggestive association with rs11856995 (score 7.13 and OR of 0.78). The C allele appears to be associated with higher odds of photic sneezing. [GWAS:Common traits (Other)]
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This snp was incorrectly associated with sneezing from light exposure also known as 'photic sneeze reflex'. Please see that page for relevant snps.
3 snps
(hide) Pick's disease
Magnitude: 0
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common in clinvar
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rs63751068, also known as G183V or Gly183Val, is a SNP in the presenilin 1 PSEN1 gene. The rare rs63751068(T) allele is considered causative for Pick's disease of the brain. [OMIM:[[Pick's disease]]]
3 snps
(hide) Polycystic kidney disease
1.3x increased risk for type-2 diabetes
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Polycystic Kidney disease rs7756992 significantly p = 0.0363 associated with type-2 diabetes in 1,630 Japanese subjects and in 1,064 controls rs7756992 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.27 (CI: 1.15-1.40, p = 9.8 x 10e-7) 1,638 type 2 diabetes patients and 1,858 controls *rs7756992 non-significant T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for *CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) *CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) *IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined...
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Although a SNP in the PKHD1 gene, this variant is considered benign in ClinVar and not causative for any disorder.
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Polycystic Kidney disease It is not clear if 23andMe is reporting on this SNP. rs398124502
normal
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Autosomal Recessive Polycystic Kidney disease also referred to as i6016633 by 23andMe
normal
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Autosomal Recessive Polycystic Kidney disease also referred to as i5000045 by 23andMe
common in complete genomics
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Although a SNP in the PKHD1 gene, this variant is considered benign in ClinVar and not causative for any disorder.
Magnitude: 0
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The A allele of this SNP is associated with autosomal recessive Polycystic Kidney disease, but it may also be protective against colorectal cancer. [OMIM:POLYCYSTIC KIDNEY DISEASE, AUTOSOMAL RECESSIVE]
15 snps
(hide) Polycystic ovary syndrome
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[GWAS:Polycystic ovary syndrome]
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[GWAS:Polycystic ovary syndrome]
Frequency: 32.3%
References:1
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[GWAS:Polycystic ovary syndrome]
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[GWAS:None]
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summary, indicating a small effect of this SNP, seen only in meta-analyses rs3792267 associated with noninsulin-dependent diabetes mellitus, polycystic ovary syndrome, type 2 diabetes, gestational diabetes and obesity [OMIM:CALPAIN 10; CAPN10]
Frequency: 56.2%
References:16
References:16
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[OMIM:TRANSCRIPTION FACTOR 7-LIKE 2; TCF7L2]
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Association study of the genetic polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene and type 2 diabetes in the Chinese population. Association of TCF7L2 polymorphisms with susceptibility to type 2 diabetes in 4,087 Japanese subjects. Exon sequencing and association analysis of polymorphisms in TCF7L2 with type 2 diabetes in a Chinese population. Meta-analysis of the association between SNPs in TCF7L2 and type 2 diabetes in East Asian population. Investigation of type 2 diabetes risk alleles support CDKN2A/B, CDKAL1, and TCF7L2 as susceptibility genes in a Han Chinese cohort. [PharmGKB:Curated Risk or phenotype-associated allele: T allele. Phenotype: Body mass index was significantly lower (p < 0.030), and cholesterol levels (p < 0.012)) were significantly higher in T2D...
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[GWAS:Polycystic ovary syndrome]
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[GWAS:Polycystic ovary syndrome]
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[GWAS:Polycystic ovary syndrome]
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Polycystic ovary syndrome [OMIM:SULFOTRANSFERASE FAMILY 2A, DEHYDROEPIANDROSTERONE-PREFERRING, MEMBER] [GWAS:Blood metabolite levels]
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A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples. [GWAS:Polycystic ovary syndrome]
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[GWAS:Polycystic ovary syndrome]
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rs1053049, rs6902123, and rs2267668 in PPARD affect Lifestyle Intervention induced changes in overall adiposity, hepatic fat storage, and relative muscle mass. Our findings provide a mechanistic explanation for the involvement of these genetic variations in the development of insulin resistance and type-2 diabetes. [OMIM:PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR-GAMMA, COACTIVATOR 1, ALPHA;]
Magnitude: 0
Frequency: 83.2%
Repute:Good
References:9
Frequency: 83.2%
Repute:Good
References:9
Magnitude: 0
Frequency: 90.3%
Repute:Good
References:7
Frequency: 90.3%
Repute:Good
References:7
common in complete genomics
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Association of polycystic ovary syndrome susceptibility single nucleotide polymorphism rs2479106 and PCOS in Caucasian patients with PCOS or hirsutism as referral diagnosis. Variants in DENND1A Are Associated with Polycystic Ovary Syndrome in Women of European Ancestry. [GWAS:None]
17 snps
(hide) Porphyria
Magnitude: 0
Repute:Good
References:1
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3 snps
(hide) Post-traumatic stress disorder
1.3x increased risk for depression
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In Caucasian non-Hispanics, the rs1360780(T) allele is associated with increased risk for depression, with an odds ratio of 1.39 (CI: 1.14-1.70, p=0.046). This same SNP, which is in the FKBP5 gene, may influence how patients respond to antidepressants including citalopram. rs1360780(T;T) homozgyotes tend to report more depressive episodes, but they also respond better to treatment with antidepressants. rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing. [PharmGKB:Curated This variant is associated with higher chance of response to anti-depressant drugs.] [OMIM:FK506-BINDING PROTEIN 5; FKBP5]
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rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing. [PharmGKB:Curated This variant is associated with higher chance of response to anti-depressant drugs.]
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rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing. Psychobiology and molecular genetics of resilience. Genetics of cortisol secretion and depressive symptoms: a candidate gene and genome wide association approach. Molecular mechanism of glucocorticoid resistance in inflammatory bowel disease. Interaction between FKBP5 and childhood trauma and risk of aggressive behavior.
more resistant to treatment for depression
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Based on a study of 256 Caucasian patients being treated for depression, carriers of a rs1049353(G) allele were less likely to respond favorably, particularly if they were females with comorbid anxiety. rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. No evidence for an involvement of variants in the cannabinoid receptor gene (CNR1) in obesity in German children and adolescents. The G1422A variant of the cannabinoid receptor gene (CNR1) is associated with abdominal adiposity in obese men. No association of...
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rs4790904 is a mutation in the gene encoding PKCα (PRKCA). It has been linked to memory capacity in healthy subjects and to risk for post-traumatic stress disorder .
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risk of the development of substance dependence significantly increased with the number of 'G' alleles at rs6454674 and SNP8 (rs806368);T/T genotypes had significant interaction effects (p = .0003 for comorbid drug dependence (DD) and alcohol dependence (AD), .0002 for DD, and .007 for AD). SNP3 and SNP8 together exerted stronger genetic effects on SD (substance dependence) than either did individually. The peak delta values among all the markers were seen for SNP3 and SNP8 (rs806368) rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD. Alcoholic patients with TGT haplotype (corresponding to rs6454674-r...
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
One copy of risk allele = associated with mildly increased chance of PTSD, hyperarousal, impaired fear discrimination in traumatized females, but not males '''Post-traumatic stress disorder is associated with PACAP and the PAC1 receptor.''' (2011). [http://www.ncbi.nlm.nih.gov/pubmed/21350482]
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An SNP in a putative estrogen response element within the ADCYAP1R1 gene. C is the risk allele - associated with PTSD, hyperarousal in females. '''Post-traumatic stress disorder is associated with PACAP and the PAC1 receptor.''' (2011). Predicts Post-traumatic stress disorder diagnoses and symptoms in females only. This may occur due to oestrogen regulation of ADCYAP1R1. Total PTSD symptoms are differentially associated with rs2267735 genotype (CC is high-risk variant) in females (p ≤ 0.001). Hyperarousal is the most robustly associated symptom with rs2267735 genotype (p = 0.0009). In a dominant/recessive model, even after controlling for childhood trauma, adult trauma, and age, genotype predicts total PTSD symptoms (p ≤ 0.001) and hyperarousal symptoms (p ≤ 0.0001). Fear...
1.4x higher schizophrenia risk
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rs6277 (957C>T, Pro319Pro) is one of several SNPs in the dopamine receptor DRD2 gene. In a study of 300+ Russian patients with schizophrenia, the rs6277(C) allele was associated with higher risk. From a pooled meta-study (total of 4 other reports plus this one) the allelic odds ratio is 1.42 (CI: 1.26-1.61, p<0.00005), and the genotypic odds ratio for the (C;C) genotype was 1.6 (CI: 1.32-1.95, p<0.00005). Note that rs6275 and rs6277 are only 18bp apart, hence their very tight linkage (r<sup>2</sup>=1). gs278 reflects a gene-gene interaction between this SNP and a NR3A SNP, rs10989591, in which older adults with a particular combination of genotypes at these two (independent) loci are reported to exhibit better episodic memory. C allele associated significantly (p = 0.0...
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[GWAS:Post-traumatic stress disorder]
complex; possible association with anxiety related behaviours
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In mice, the genetic locus best correlated to anxiety-related behaviour contains the 'regulator of G protein signaling 2' gene . In humans, SNPs in the equivalent RGS2 gene have now been studied to see if they are correlated to anxiety related disorders. In the first part of one study, 119 families including children underwent standard lab-based behavioural assessments of behavioural inhibition, defined as a heritable temperamental profile characterized by a tendency to be shy, avoident, and behaviourally restrained in situations that are novel or unfamiliar. Along with some other RGS2 SNPs, carriers of a rs4606(G) allele were 3 fold more likely to exhibit behavioural inhibition (CI: 1.31-6.84, p = 0.0026). In the second part of this study, 744 college undergraduates (228 men, 516 women) w...
11 snps
(hide) Pre-eclampsia
~1.4x increased risk of hypertension
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rs5186, a SNP known as +1166A/C or A1166C, is located in the 3' untranslated region of the angiotensin II receptor type 1 gene AGTR1, which is also known as AT2R1 or AT1R. It is among the most studied of over 50 SNPs in AGTR1. The rs5186(C) allele is associated with increased risk for essential hypertension in Caucasian populations with an odds ratio of 7.3 (homozygote (C;C) compared to (A;C) and (A;A), CI: 1.9-31.9,p=0.0015). There are likely to be ethnic differences in risk; while the rs5186(C) allele was associated with hypertension in a Chinese population , it was not been observed as a risk in a Japanese population. Age and gender may also influence risk, as discussed in a review of AGTR1 SNPs and their role in hypertension and related disorders. Pregnant women who are rs5186(C) allel...
increased risk of hypertension
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rs699 is a SNP in the angiotensin AGT gene that encodes a functional change. In most published literature, the name for this SNP is M235T, or perhaps Met235Thr, however its amino acid 268 (not 235) that varies based on the numbering in todays databases. rs699 is also occasionally known as C4072T. In any case, the rs699(C) allele encodes the threonine variant, which is associated with higher plasma angiotensin levels, and ultimately higher blood pressure leading to increased risk for hypertension associated disorders. This association was first reported in 1992 , and many studies, though not all, have replicated these findings. rs699 is also (generally) reported to be in tight linkage with rs5051, a neighboring SNP in the promoter of the AGT gene. rs699(C) has also been implicated as a risk...
1.6x increased risk for preeclampsia in most populations Note: this is relevant to the fetal genotype, not the maternal genotype
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rs2549782 is a SNP in the endoplasmic reticulum aminopeptidase 2 ERAP2 gene. A case-control study of 1103 Chilean maternal-fetal dyads and 1637 unpaired African American samples (836 maternal, 837 fetal) concluded that the fetal minor allele rs2549782(G) was associated with 1.3x increased risk (CI: 1.075-1.619) for pre-eclampsia in the African American population (p = 0.009), but not in the Chilean population. }}
Frequency: 17.7%
References:1
References:1
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[GWAS:Preeclampsia]
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[GWAS:Preeclampsia]
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[GWAS:Preeclampsia]
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This SNP is located on chromosome 2q22-23, in the activin receptor type 2 gene (ACVR2A) gene. A study of 1139 Norwegian women with one or more pre-eclamptic pregnancies and 2269 controls (women with normal pregnancies) identified four SNPs in this region (rs1424941, rs1014064, rs2161983 and rs3768687) as associated with higher risk for pre-eclampsia.
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This SNP is located on chromosome 2q22-23, in the activin receptor type 2 gene (ACVR2A) gene. A study of 1139 Norwegian women with one or more pre-eclamptic pregnancies and 2269 controls (women with normal pregnancies) identified four SNPs in this region (rs1424941, rs1014064, rs2161983 and rs3768687) as associated with higher risk for pre-eclampsia. Association between the candidate susceptibility gene ACVR2A on chromosome 2q22 and pre-eclampsia in a large Norwegian population-based study (the HUNT study). Genetic association of the activin A receptor gene (ACVR2A) and pre-eclampsia.
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This SNP is located on chromosome 2q22-23, in the activin receptor type 2 gene (ACVR2A) gene. A study of 1139 Norwegian women with one or more pre-eclamptic pregnancies and 2269 controls (women with normal pregnancies) identified four SNPs in this region (rs1424941, rs1014064, rs2161983 and rs3768687) as associated with higher risk for pre-eclampsia.
Frequency: 82.3%
References:1
References:1
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[GWAS:Preeclampsia]
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[GWAS:Preeclampsia]
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[GWAS:Preeclampsia]
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
normal risk
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rs4762, a SNP in the angiotensin II AGT gene, has been reported to be associated with increased risk for developing pre-eclampsia, based on a study of ~180 French-Canadian women. The odds ratio associated with the rs4762(T) allele (encoding methionine) was 1.9 (CI:1.2–2.9, p=0.0033). Note that rs4762 is commonly referred to in the literature as 'T174M' or 'Thr174Met'; however, databases now indicate that the amino acid that varies is #207 (not 174), as the protein is currently numbered. rs4762 was also reported to play the major role in the 2.1 fold increased risk (CI: 1.4-3.4, p=0.0008) for pre-eclampsia of the rs3889728(A)-rs4762(T)-rs699(C) haplotype. Correction of population stratification in large multi-ethnic association studies. Ten renin-angiotensin system-relate...
Magnitude: 0
Frequency: 90.3%
Repute:Good
References:1
Frequency: 90.3%
Repute:Good
References:1
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[GWAS:Preeclampsia]
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[GWAS:Preeclampsia]
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
17 snps
(hide) Premature birth
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A study of maternal and fetal DNA from 370 US Caucasian birth-events (172 cases and 198 controls) concluded that the single strongest effect observed in maternal DNA was for SNP rs879293, with a significant allelic (p = 2.30x10e-3) and genotypic association (p = 2.0x10e-6) with spontaneous preterm birth (PTB). The odds ratio for this SNP was 2.80 (CI:1.77-4.44) under a recessive model.
Frequency: 78.8%
References:0
References:0
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A study of maternal and fetal DNA from 370 US Caucasian birth-events (172 cases and 198 controls) concluded that the single strongest effect in fetal DNA was associated with rs17121510 in the interleukin-10 receptor antagonist (IL-10RA) gene at both allelic (p = 0.01) and genotypic (p = 3.34x10e-4) levels. The odds ratio for preterm birth for the genotypic additive model was 1.92 (CI: 1.15-3.19, p = 2.00x10e-3). Role of polymorphic variants as genetic modulators of infection in neonatal sepsis.
common in complete genomics
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Women with the snp has been linked to significant risk of a premature birth These press releases explain it more simply The risky variation is 3x more common in women of african descent. *rs2298668 Prolylcarboxypepdiase E112D (rs2298668)D allele alone and jointly with chronic hypertension were associated with a significantly increased risk of preeclampsia Polymorphism in maternal LRP8 gene is associated with fetal growth.
normal
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rs4986790, a SNP also known as Asp299Gly (and also 896A/G) in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in th...
normal
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rs4986791, a SNP also known as Thr399Ile (and also 1196C/T) in the TLR4 gene, is often studied along with a cosegregating SNP known as Asp299Gly, rs4986790. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986791 is (T). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in t...
5 snps
(hide) Primary biliary cirrhosis
Magnitude: 2
Frequency: 21.2%
Repute:Bad
References:29
Frequency: 21.2%
Repute:Bad
References:29
2x increased risk of developing SLE; 1.6x increased risk of developing primary biliary cirrhosis; and 1.7x increased risk of developing Sjögren's syndrome
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rs10488631, a SNP located 3' of the IRF5 gene, has been reported as a possibly causative SNP for systemic lupus erthymatosus (SLE), based on a study of ~700 Swedish patients. The risk allele is rs10488631(C), with a reported odds ratio of 2.07 (CI: 1.63-2.62, p = 9x10e-10). The C allele is also associated with primary biliary cirrhosis, with each C increasing the odds about 1.6 times. Each C allele increases risk of Sjögren's syndrome by 1.7 times. SLE rs10488631 and rs7582694 [OMIM:INTERFERON REGULATORY FACTOR 5; IRF5] [GWAS:Systemic lupus erythematosus]
1.54x chance of developing primary biliary cirrhosis.
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23andMe blog *Each G at rs2856683 increased the odds of primary biliary cirrhosis by 1.75x. *Each G at rs6441286 increased the odds of primary biliary cirrhosis by 1.54x. *Each A at rs3790567 increased the odds of primary biliary cirrhosis by 1.51x. [PharmGKB:Curated A GWAS of 2072 Canadian and U.S. subjects (536 patients with primary biliary cirrhosis and 1536 controls) showed that primary biliary cirrhosis was significantly and reproducibly associated with this SNP (rs6441286) at the IL12A locus (P=2.42x10(-14); odds ratio, 1.54).] [OMIM:?] [GWAS:Primary biliary cirrhosis]
Slightly increased risk of developing primary biliary cirrhosis
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[OMIM:?] [GWAS:Primary biliary cirrhosis]
Normal risk of developing primary biliary cirrhosis
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On the association between rheumatoid arthritis and classical HLA class I and class II alleles predicted from single-nucleotide polymorphism data. A two-stage search strategy for detecting multiple loci associated with rheumatoid arthritis. [GWAS:Primary biliary cirrhosis]
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The G allele is associated with 1.3 times higher odds of primary biliary cirrhosis. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. Primary Biliary Cirrhosis: Preliminary Research [GWAS:Celiac disease]
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[GWAS:Primary biliary cirrhosis]
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23andMe blog *Each G at rs2856683 increased the odds of primary biliary cirrhosis by 1.75x. *Each G at rs6441286 increased the odds of primary biliary cirrhosis by 1.54x. *Each A at rs3790567 increased the odds of primary biliary cirrhosis by 1.51x. Vaccine immunogenetics: bedside to bench to population. Replicated association of 17q12-21 with susceptibility of primary biliary cirrhosis in a Japanese cohort. A GWAS follow-up study reveals the association of the IL12RB2 gene with systemic sclerosis in Caucasian populations. Primary Biliary Cirrhosis: Preliminary Research [PharmGKB:Curated A GWAS of 2072 Canadian and U.S. subjects (536 patients with primary biliary cirrhosis and 1536 controls) showed that primary biliary cirrhosis was significantly and reproducibly associated with this SNP ...
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23andMe blog *Each G at rs2856683 increases the odds of primary biliary cirrhosis by 1.75x. *Each G at rs6441286 increased the odds of primary biliary cirrhosis by 1.54x. *Each A at rs3790567 increased the odds of primary biliary cirrhosis by 1.51x. Primary Biliary Cirrhosis: Preliminary Research [OMIM:?]
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[GWAS:Primary biliary cirrhosis]
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[GWAS:Primary biliary cirrhosis]
Normal risk of developing primary biliary cirrhosis
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Each A allele of this SNP in the SPIB gene is associated with 1.46 times higher odds of primary biliary cirrhosis. [GWAS:Primary biliary cirrhosis]
normal risk of rheumatoid arthritis, SLE, Sjögren's syndrome, type-1 diabetes, and primary biliary cirrhosis.
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune dise...
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[GWAS:None]
Normal risk of developing primary biliary cirrhosis
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[GWAS:Primary biliary cirrhosis]
14 snps
(hide) Primary hyperoxaluria
References:0
References:2
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[OMIM:?]
common/normal
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Primary hyperoxaluria type 2 Note: 23andMe may have discontinued reporting results for this SNP, as several Promethease users have reported it is not included in their data. rs80356708
common/normal
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Primary hyperoxaluria type 2 Note: 23andMe may have discontinued reporting results for this SNP, as several Promethease users have reported it is not included in their data. rs180177309
4 snps
(hide) Primary sclerosing cholangitis
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via spitoon reports about which identifies 32 snps relevant to Crohn's disease: '''Out of a possible total of 46, 80% of people will have between 17 and 25 copies of the riskier versions of these SNPs. Because there are so many of these SNPs--and because the riskier versions are often more common than their less risky counterparts--even people at the high end of the distribution are not much more likely than average to develop Crohn's disease.''' *rs3197999 A 1.2 *rs2188962 T 1.25 *rs2476601 G 1.31 *rs2274910 C 1.14 *rs9286879 G 1.19 *rs10045431 C 1.11 *rs6908425 C 1.21 *rs2301436 T 1.21 *rs1456893 A 1.2 *rs1551398 A 1.08 *rs10758669 C 1.12 *rs3764147 G 1.25 *rs2872507 A 1.12 *rs744166 A 1.18 *rs762421 G 1.13 *rs3763313 C 1.19 Proxy snps on 23andMe *rs7714584 G 1.33 *rs6478108 T 1.22 *rs12...
Frequency: 44.2%
References:4
References:4
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[OMIM:INFLAMMATORY BOWEL DISEASE 1; IBD1]
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[GWAS:None]
5 snps
(hide) Progressive supranuclear palsy
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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The C allele of this SNP in the NR1H3 gene is associated with increased (but still low) risk of progressive supranuclear palsy. [PharmGKB:Non-Curated GWAS results: Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. (Initial Sample Size: 4,763 individuals; Replication Sample Size: NR); (Region: 11p11.2; Reported Gene(s): NR1H3; Risk Allele: rs7120118-G); (p-value= 0.00000004).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
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Each copy of the G version of rs8070723 was associated with about 5.5 times lower odds of progressive supranuclear palsy. The researchers identified smaller effects at rs1411478, rs7571971 and rs1768208. 23andMe blog Genomewide association study for susceptibility genes contributing to familial Parkinson disease. Genome-wide association study confirms SNPs in SNCA and the MAPT region as common risk factors for Parkinson disease. [GWAS:None]
5 snps
(hide) Prostate cancer
1.6x increased risk for prostate cancer; also other cancers 1.4 times as likely to develop colorectal cancer
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. This SNP has also been reported to influence the cancer-risk-decreasing effect of aspirin. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neig...
Magnitude: 2.5
Frequency: 51.3%
Repute:Bad
References:1
Frequency: 51.3%
Repute:Bad
References:1
1.39x increased risk for PCSM in patients with prostate cancer For a person already diagnosed with prostate cancer, this relatively common genotype is associated with a more aggressive form of the cancer and an increased risk (by 1.39x) of dying from causes related to the cancer.
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rs11672691 is a SNP on chromosome 19 located between the ATP5SL and CEACAM21 genes and within LOC100505495, a possible noncoding RNA. A large study of over 10,000 patients with prostate cancer concluded that each rs11672691(G) allele was associated with an increased risk (by 1.18x) of prostate cancer specific mortality (PCSM), i.e. death from the cancer. A meta-analysis of 4 studies totaling ~6000 patients with prostate cancer and follow up in 49,000 samples concluded that rs11672691 was associated with increased susceptibility (odds ratio 1.12, CI:1.03–1.21, p = 1.4 x 10e-8) but also with aggressive prostate cancer and therefore a poorer prognosis. [GWAS:Prostate cancer]
1.38x increased risk for prostate cancer
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rs4430796 is a SNP in the TCF2 gene on chromosome 17q12, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs4430796 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On its own, the rs4430796(A;A) risk genotype - in dbSNP orientation, not as published - yields an odds ratio for developing prostate cancer of 1.38 (CI: 1.21-1.57, p=1.6x10e-6) and may account for 10.2% of population attributable risk. article linking to Prostate cancer and type-2 diabetes 403 non-Hispanic white families were studied, totaling 1,015 men, to reach the conclusion that the rs4430796(A) allele is associated with increased prostate cancer risk; the odds ratio was 1.40 (CI: 1.09-1.81) ...
1.7x increased risk for prostate cancer
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rs7837688 is one of 4 tightly linked SNPs in the 'locus 1' region of 8q24 chromosomal region, which has been linked in several studies to prostate cancer, initially through rs1447295. In a study of 1,563 patients of European ancestry, the odds ratio for prostate cancer associated with risk genotypes of locus 1 were reported as 1.70 (CI: 1.39-2.07). Two other regions of chromosome 8q24 were also studied. [GWAS:None]
Increased risk of developing prostate cancer
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'''rs1691053''' is located on chromosome 5p15.31 and is associated with SRD5A1, which encodes the 5α-reductase isoform 1. This SNP has shown to be associated with prostate cancer (PCA), which is affected by dihydrotestosterone (DHT), the most potent male hormone. DHT functions by directly activating the androgen receptor. SRD5A along with another steroid-5α-reductase gene, HSD3B1 located on chromosome 1p12, are involved with converting testosterone to the more potent androgen DHT. In 2010, Setlur et al. investigated the associations between SNPs in genes, HSD3B1, SRD5A1/2, and AKR1C2, that are involved in converting testosterone to DHT and known to confer PCA risk. The cohort consisted of 426 men, 205 controls and 221 cases. They were selected based on a prostate-specific antigen screening...
Magnitude: 2
Frequency: 30.1%
Repute:Bad
References:106
Frequency: 30.1%
Repute:Bad
References:106
1.3x increased type-2 diabetes risk
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This SNP is in the TCF7L2 gene, and has been linked to type-2 diabetes, breast cancer and aggressive prostate cancer. This SNP is also known as IVS4G>T. is the paper which links it to Breast cancer. It suggests the T allele as increasing risk. reports the association of rs12255372 and rs7903146 with Type-2 diabetes in a Finnish sample. rs12255372 Common variants (rs12255372 and rs7903146) in TCF7L2 seem to be associated with an increased risk of diabetes among persons with impaired glucose tolerance Considered for type-2 diabetes with rs7903146 rs12255372 rs10885406. Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion as measured by acute insulin response and adjusted for the degree of insulin sensitivity (p = 0.036). In a study of 1,457 prostate cancer case...
somewhat higher risk for prostate cancer
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rs629242 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (T); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=7.2 x 10e-7, using an additive model of risk.
Magnitude: 2
Frequency: 47.8%
Repute:Bad
References:6
Frequency: 47.8%
Repute:Bad
References:6
1.7x increased risk for prostate cancer
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rs10086908 is a SNP in the 8q24 chromosomal region, which has been linked in several studies to prostate cancer. In a study of 1,563 patients of European ancestry, rs10086908 was designated as the representative of a prostate cancer risk region termed 'locus 3', with an odds ratio of 1.70 (CI: 1.39-2.07) for carriers of a risk genotype. Two other regions of chromosome 8q24 were also studied. Confirmation study of prostate cancer risk variants at 8q24 in African Americans identifies a novel risk locus. Homozygous deletions and recurrent amplifications implicate new genes involved in prostate cancer.
1.6x increased prostate cancer risk
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This SNP is upstream of the IL10 gene, and is also known as the -1082G>A IL10 SNP. Dust mite exposure modifies the effect of functional IL10 polymorphisms on allergy and asthma exacerbations. Dust mite exposure significantly modified the relation between 3 SNPs in IL10 (rs1800896, rs3024492, and rs3024496). Homozygosity for the minor allele of each of the 3 SNPs was associated with increased risk of occurrence ( approximately 3-fold to 39-fold increase). A study of 258 prostate cancer cases concluded that the rs1800896(A) allele, known to result in lower levels of this anti-inflammatory cytokine, was positively associated with risk (AG vs. GG, odds ratio of 1.69, CI: 1.10-2.60; AA vs. GG, OR of 1.81, CI: 1.11-2.96).
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
Magnitude: 1.5
Frequency: 43.4%
Repute:Bad
References:55
Frequency: 43.4%
Repute:Bad
References:55
increased prostate cancer risk (odds ratio 1.2) Compared to the (C;C) genotype for this SNP, (C;T) genotypes are estimated to be at 1.2x increased risk for prostate cancer.
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rs10993994 linked to prostate cancer cancer-genetics these snps influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 [PharmGKB:Non-Curated GWAS Results: Multiple loci identified in a genome-wide association study of prostate cancer (Initial Sample Size: 1,172 cases, 1,157 controls; Replication Sample Size: 3,941 cases, 3,964 controls; Risk Allele: rs10993994-T).] [OMIM:MICROSEMINOPROTEIN, BETA; MSMB] [GWAS:Prostate cancer] [GWAS:Prostate cancer (aggressive)]
1.5x increased prostate cancer risk
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rs486907 is a SNP in the RNase L RNASEL gene that has been associated with cancer risk. The basic rationale behind most of these studies is that RNase L is responsible for deactivating RNA-based viruses that are associated with certain cancers, and therefore SNPs that lead to lower RNase L activity may lead to increased cancer risk. This SNP is also known as R462Q or Arg462Gln. In a study of prostate cancer patients, rs486907(A;G) heterozygotes were calculated to be at 1.5x increased risk, and rs486907(A;A) homozygotes 2x risk (p=0.007). This SNP was also associated with hereditary-prostate-cancer (HPC) predisposition with an odds ratio of 1.97 (p=0.07) in a study of 116 affected Finnish families. See also: [OMIM:PROSTATE CANCER, SUSCEPTIBILITY TO]
Magnitude: 1.5
Frequency: 63.3%
Repute:Bad
References:1
Frequency: 63.3%
Repute:Bad
References:1
Slightly increased risk of developing prostate cancer
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rs13149290 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (C); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=2.5 x 10e-5, using a dominant model of risk.
1.3x higher risk for endometrial cancer (in Chinese women)
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Category:interestingrs34330 shows an association with breast cancer in a British study involving ~2300 patients. The odds ratio for the (T;T) vs (C;C) homozygotes is 1.22 (CI: 1.02-1.47, p=0.013). found a significant association between rs34330 (-79C/T) and prostate cancer found higher odds for endometrial cancer among 1,200+ Chinese patients associated with rs34330, with an odds ratio of 1.33 (CI: 1.06-1.66) and 1.51 (CI: 1.16-1.94) for the (C;T) and (T;T) genotypes, respectively, compared with the (C;C) genotype. see also omim 176807 [OMIM:CYCLIN-DEPENDENT KINASE INHIBITOR 1B; CDKN1B] [GWAS:Systemic lupus erythematosus]
complex! see rs4880
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The rs4880(T) allele, part of the codon for amino acid valine at codon 16 of the antioxidant protein from the mitochrondrial superoxide dismutase 2 SOD2 gene, is the most common in most populations studied. The rs4880(C) allele gives rise to an alanine at this position is it also known as Val16Ala manganese superoxide dismutase, or A16V. There appears to be some conflict in the literature over the effect of this SNP. Having a valine at codon 16 is said to reduce enzyme activity , and thus lead to increased oxidative stress, yet in at least one study of the actual enzyme levels measured in people, SOD2 activity was 33% higher in (C;T) or (T;T) individuals compared to (C;C) individuals . Regardless of how this resolves, several phenotypic associations have been reported for this SNP, includi...
Frequency: 1.8%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study (Initial Sample Size: 1,345 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Prostate cancer.] [GWAS:Prostate cancer]
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[PharmGKB:Non-Curated GWAS Results: Multiple loci identified in a genome-wide association study of prostate cancer (Initial Sample Size: 1,172 cases, 1,157 controls; Replication Sample Size: 3,941 cases, 3,964 controls; Risk Allele: rs4962416-C).] [GWAS:Prostate cancer (aggressive)]
Frequency: 16.1%
References:9
References:9
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[GWAS:None]
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[GWAS:Prostate cancer]
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[GWAS:Prostate cancer]
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cancer-genetics these snps influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 [PharmGKB:Non-Curated GWAS Results: Multiple newly identified loci associated with prostate cancer susceptibility (Initial Sample Size: 1,854 cases, 1,894 controls; Replication Sample Size: 3,268 cases, 3,366 controls; Risk Allele: rs6465657-C).] [OMIM:LEMUR TYROSINE KINASE 2; LMTK2] [GWAS:Prostate cancer] [GWAS:Prostate cancer]
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rs2070874 is a SNP in the promoter region of the interleukin 4 IL4 gene. This SNP is one of five SNPs reported to be useful in a SNP set defining the risk of dying from prostate cancer among patients with the disease; see gs242 and gs243. Visceral leishmaniasis (VL) caused by Leishmania chagasi is endemic to northeast Brazil. A positive delayed-type hypersensitivity skin test response (DTH+) is a marker for acquired resistance to disease. the DTH- phenotype was associated with SNP rs2070874 at IL4 (OR 3.14; P=0.006; 95% CI=1.38-7.14), and SNP rs30740 between LECT2 and TGFBI (OR 3.00; P=0.042; 95% CI=1.04-8.65)
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A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study [PharmGKB:Non-Curated GWAS results: A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study (Initial Sample Size: 1,345 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Prostate cancer.] [GWAS:Prostate cancer]
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rs6501455 increases susceptibility to Prostate cancer 1.14 times for carriers of the A allele Meta-analysis of genome-wide and replication association studies on prostate cancer. GWAS SNP Replication among African American and European American men in the North Carolina-Louisiana prostate cancer project (PCaP).
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[GWAS:Prostate cancer]
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[PharmGKB:Non-Curated GWAS results: A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study (Initial Sample Size: 1,345 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Prostate cancer.] [GWAS:Prostate cancer]
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related to Prostate cancer] and Type-2 diabetes The increased risk associated with rs7501939 and the closely linked rs4430796 is approximately doubled in individuals hereditarily predisposed to develop early-onset prostate cancer, based on a study of ~1,000 men. rs7501939 identified as one of three HNF1B gene SNPs associated with decreased risk for prostate cancer in two large prospective studies cancer-genetics these SNPs influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 [OMIM:PROSTATE CANCER, HEREDITARY, 11; HPC11] [GWAS:Prostate cancer]
Magnitude: 1
Frequency: 29.2%
Repute:Good
References:1
Frequency: 29.2%
Repute:Good
References:1
Normal risk of developing prostate cancer
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rs10492519 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (G); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=5.6 x 10e-6, using an additive model of risk.
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prostate cancer treatment response rs2279115 and rs7121 Complex haplotype structure of the human GNAS gene identifies a recombination hotspot centred on a single nucleotide polymorphism widely used in association studies. Polymorphism in maternal LRP8 gene is associated with fetal growth. Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PTHR1 mutations associated with Ollier disease result in receptor loss of function. Functional genetic polymorphisms and female reproductive disorders: Part I: Polycystic ovary syndrome and ovarian response. A sensitive functional assay reveals frequent loss of genomic imprinting in human placenta. Association of the GNAS locus with severe malaria. Dev...
Frequency: 31.0%
References:0
References:0
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association with prostate cancer
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rs2470152 is clearly associated with serum E2 and E1 levels in men, influencing risk of many conditions including prostate cancer, breast cancer and osteoporosis
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A study of ~500 Japanese prostate cancer patients found that individuals with a rs2011077(G;G) genotype had a 6.2- and 3-fold increased risk of prostate cancer and benign prostate hyperplasia (BPH), and a 5.5-fold increased risk of metastatic prostate cancer, compared to the (A;A) genotype.
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[GWAS:Prostate cancer]
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rs2107301 is a SNP in the vitamin D VDR receptor gene. rs2107301(T;T) homozygotes were associated with an ~2.5x higher risk of prostate cancer compared to homozygote carriers of the more common (C) allele in the 630 Caucasian patients studied.
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rs1442295 is a SNP in chromosome 8q24, region 1, associated both with overall risk for prostate cancer as well as disease severity, based on a meta-analysis across 10 studies.
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(rs2171492, Cys303Gly) in CPA4 was associated with an increased risk of aggressive prostate cancer among younger ...
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prostate cancer rs3212649 (OR=1.67 (1.07-2.6), P=0.0009) and rs1126643 (OR=1.52 (1.01-2.28), P=0.0088).
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[GWAS:Prostate cancer]
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[GWAS:Prostate cancer]
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[GWAS:None]
Frequency: 40.7%
References:4
References:4
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[GWAS:Prostate cancer]
Normal risk of prostate cancer
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Sequence variants of elaC homolog 2 (Escherichia coli) (ELAC2) gene and susceptibility to prostate cancer in the Health Professionals Follow-Up Study. Development of a fingerprinting panel using medically relevant polymorphisms. Genetic variants and prostate cancer risk: candidate replication and exploration of viral restriction genes. Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project. [OMIM:PROSTATE CANCER, SUSCEPTIBILITY TO]
Frequency: 42.0%
References:14
References:14
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Chinese breast cancer rs11568818(G;G) significantly worse prognosis (OS HR: 6.7, 95% CI: 2.4-18.6) than patients homozygous for the common allele (A) [GWAS:Prostate cancer]
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cancer-genetics these snps influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 [PharmGKB:Non-Curated GWAS Results: Multiple newly identified loci associated with prostate cancer susceptibility (Initial Sample Size: 1,854 cases, 1,894 controls; Replication Sample Size: 3,268 cases, 3,366 controls; Risk Allele: rs9364554-T).] [GWAS:Prostate cancer]
1.36x risk for prostate cancer
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In a study of ~1000 Caucasian patients with prostate cancer, rs1571801 was the SNP most associated with not only prostate cancer, but having an aggressive form of it. The odds ratio for aggressive prostate cancer associated with the risk allele, rs1571801(A), was 1.36 (CI: 1.13 - 1.65, p = 0.001). The odds ratio associated with (nonaggressive) prostate cancer was also higher than average for this SNP; for the same (A) risk allele, it was 1.27 (CI: 1.10 - 1.48, p = 0.0017). Although the association was found in a study of Caucasian patients, it was also reported to be statistically significant in a population of 210 African-Americans with prostate cancer. According to 'The odds ratio for aggressive prostate cancer ranged from 1.29 to 1.50 in men with one or two copies of the mutant A allele...
Frequency: 45.5%
References:1
References:1
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[GWAS:Prostate cancer]
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cancer-genetics these snps influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 rs7931342 showed some evidence of association with breast cancer (per minor allele OR, 0.95; 95% CI, 0.91-0.99; P(trend) = 0.028) Multiple novel prostate cancer predisposition loci confirmed by an international study: the PRACTICAL Consortium. Prostate cancer genomics: towards a new understanding. Generalizability of associations from prostate cancer genome-wide association studies in multiple populations. Analysis of recently identified prostate cancer susceptibility loci in a population-based study: associations with family history and clinical features. Two indepe...
Frequency: 46.2%
References:18
References:18
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rs13254738 increases susceptibility to Prostate cancer 1.18 times for carriers of the C allele [PharmGKB:Curated A study in a series of 1,499 breast cancer cases and 1,390 controls showed an association between rs13281615 (at 8q24) and risk of breast cancer.] [GWAS:Prostate cancer]
Frequency: 46.4%
References:21
References:21
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nature identifies rs10486567 rs10993994 rs10896449 in prostate cancer [PharmGKB:Non-Curated GWAS Results: Multiple loci identified in a genome-wide association study of prostate cancer (Initial Sample Size: 1,172 cases, 1,157 controls; Replication Sample Size: 3,941 cases, 3,964 controls; Risk Allele: rs10896449-G).] [OMIM:PROSTATE CANCER, HEREDITARY, 14; HPC14] [GWAS:Prostate cancer (aggressive)]
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Two genetic markers in the 8q24 region of chromosome 8 rs7008482 and rs16901979 have been linked to an increased risk of prostate cancer in African Americans. abstract
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Associated with prostate cancer Multiple novel prostate cancer predisposition loci confirmed by an international study: the PRACTICAL Consortium. Generalizability of associations from prostate cancer genome-wide association studies in multiple populations. Replication of the 10q11 and Xp11 prostate cancer risk variants: results from a Utah pedigree-based study. Meta-analysis of genome-wide and replication association studies on prostate cancer. Validation of genome-wide prostate cancer associations in men of African descent. Characterizing associations and SNP-environment interactions for GWAS-identified prostate cancer risk markers--results from BPC3. [PharmGKB:Curated GWAS Results: Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer (Initial Sample Size...
Frequency: 47.8%
References:2
References:2
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[GWAS:Prostate cancer]
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[GWAS:Prostate cancer]
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[GWAS:Prostate cancer]
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[GWAS:Prostate cancer]
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18067C>T possibly related to non-Hodgkin lymphoma rs2040639-AG, contribute to oral cancer risk. pseudo-haplotype with AG-CC genotypes in *2.45x risk rs2040639-rs861539 *5.03x risk rs2040639-rs861539-rs2075685 *10.10x risk rs2040639-rs861539-rs2075685-rs1799782 rs4880(C;T) prostate cancer patients being treated by radiation therapy are more likely (8% compared to 0%, p=0.02) to exhibit a significant increase in grade 2 late rectal bleeding after irradiation than (C;C) or (T;T) patients, based on a study of 135 patients. The odds for this are worse if the patient also has the rs861539(C;T) genotype (14% vs 1%, p=0.002). [OMIM:?]
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cancer-genetics these snps influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 Multiple independent genetic variants in the 8q24 region are associated with prostate cancer risk. Pooled analysis of genetic variation at chromosome 8q24 and colorectal neoplasia risk. Prostate cancer risk associated loci in African Americans. Estimation of genotype relative risks from pedigree data by retrospective likelihoods. Meta-analysis of genome-wide and replication association studies on prostate cancer. Characterizing associations and SNP-environment interactions for GWAS-identified prostate cancer risk markers--results from BPC3. [GWAS:Prostate cancer]
Frequency: 54.5%
References:2
References:2
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[GWAS:Prostate cancer]
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[GWAS:Prostate cancer]
Frequency: 57.1%
References:1
References:1
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news rs12329760(T) associated with TMPRSS2-ERG fusion by translocation (p=0.05) and with multiple copies of the gene fusion (p=0.03) relevant to metastatic prostate cancer.
Frequency: 57.5%
References:24
References:24
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nature identifies rs10486567 rs10993994 rs10896449 in prostate cancer [PharmGKB:Non-Curated GWAS Results: Multiple loci identified in a genome-wide association study of prostate cancer (Initial Sample Size: 1,172 cases, 1,157 controls; Replication Sample Size: 3,941 cases, 3,964 controls; Risk Allele: rs10486567-G).] [OMIM:JUXTAPOSED WITH ANOTHER ZINC FINGER GENE 1; JAZF1] [GWAS:Prostate cancer (aggressive)]
Frequency: 57.5%
References:12
References:12
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rs11649743 identified as one of three HNF1B gene SNPs associated with decreased risk for prostate cancer in two large prospective studies prostate cancer rs4430796 and rs11649743 in multiple populations, with P = 1.7 x 10(-9) [PharmGKB:Curated In a fine-mapping study in the HNF1B gene at 17q12 this variant was associated with prostate cancer risk.] [OMIM:PROSTATE CANCER, HEREDITARY, 11; HPC11]
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rs887391 was the most strongly associated SNP in the 19q13 region, which was a region highly associated with prostate cancer (p=9.4 x 10(-4)) based on two large studies. Individual and cumulative effect of prostate cancer risk-associated variants on clinicopathologic variables in 5,895 prostate cancer patients. Prostate cancer risk associated loci in African Americans.
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[OMIM:?] [GWAS:Prostate cancer]
normal
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In seven different populations studied, rs9623117(C) was consistently higher in aggressive prostate cancer cases than in controls (p = 5.0 x 10e-7). The odds ratio (OR) of allele C for aggressive prostate cancer was estimated to be 1.18 (CI: 1.11-1.26). This SNP was also associated with increased risk for nonaggressive prostate cancer, with an odds ratio of 1.11 (CI: 1.04 - 1.19, p = 0.004). [PharmGKB:Non-Curated GWAS results: Sequence variants at 22q13 are associated with prostate cancer risk. (Initial Sample Size: 1,235 aggressive cases, 1,599 controls; Replication Sample Size: 3,629 aggressive cases, 4,255 non-aggressive cases, 5,738 controls); (Region: 22q13.1; Reported Gene(s): TNRC6B; Risk Allele: rs9623117-C); (p-value= 0.0000005).This variant is associated with Prostate cancer.]
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[GWAS:Prostate cancer]
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[PharmGKB:Non-Curated GWAS results: A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study (Initial Sample Size: 1,345 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Prostate cancer.] [GWAS:Prostate cancer]
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[GWAS:Prostate cancer]
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rs1930293 increases susceptibility to prostate cancer 1.20 times for heterozygotes (AG) and 1.70 times for homozygotes (GG)
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[GWAS:Prostate cancer]
Frequency: 69.0%
References:1
References:1
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[GWAS:Prostate cancer]
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[GWAS:Prostate cancer]
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[GWAS:Prostate cancer]
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[GWAS:Prostate cancer]
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rs2710646(A) had an OR of 1.16 (P = 7.79x10-4) for all Icelandic prostate cancer cases
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[GWAS:Prostate cancer]
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rs902774 increases susceptibility to Prostate cancer 1.34 times for heterozygotes (AG) and 2.29 times for homozygotes (AA) Correcting 'winner's curse' in odds ratios from genomewide association findings for major complex human diseases. [GWAS:None]
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cancer-genetics these snps influence genetic risk for prostate cancer rs2660753 showed a per-allele OR, 1.08 (95% confidence interval, 1.00-1.16; P = 0.06) An initial report of an association with between this SNP and risk for ovarian cancer was not replicated when the same authors expanded the study over 12 studies comprising 4,482 cases (and over 6,000 controls). [GWAS:Prostate cancer]
Frequency: 86.7%
References:1
References:1
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[GWAS:Prostate cancer]
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prostate cancer rs3212649 (OR=1.67 (1.07-2.6), P=0.0009) and rs1126643 (OR=1.52 (1.01-2.28), P=0.0088).
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Implications for prostate cancer of IGF1 the TCC haplotype and the rs6220 SNP were associated with elevated levels of circulating IGF1 (p = 0.001 and <0.0001, respectively) Common genetic variation in the IGF-1 gene, serum IGF-I levels and breast density. IGF-I and IGF-II genetic variation and breast cancer risk in Chinese women: results from the Shanghai Breast Cancer Study. Genetic polymorphisms involved in insulin-like growth factor (IGF) pathway in relation to mammographic breast density and IGF levels. Genetic variation in insulin-like growth factors and brain tumor risk. Can genes for mammographic density inform cancer aetiology? Genotypes and haplotypes in the insulin-like growth factors, their receptors and binding proteins in relation to plasma metabolic levels and mammographic...
normal risk
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rs1859962 is a SNP on chromosome 17q24.3, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs1859962 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On its own, the rs1859962(G;G) risk genotype yields an odds ratio for developing prostate cancer of 1.28 (CI: 1.11-1.47, p=5.5x10e-4) and may account for 6.5% of population attributable risk. news linked to Prostate cancer and type-2 diabetes cancer-genetics these snps influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 [PharmGKB:Curated GWAS Results: Two variants ...
normal
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rs351855, a SNP in the fibroblast growth factor receptor 4 (FGFR4) gene, is also known as the Gly388Arg variant. The rs351855(T) allele encodes the risk (Arg) allele. The Arg form of this SNP is likely to cause a harder to treat version of node-positive breast cancer, including reducing the efficacy of Herceptin, based on a study of 372 patients. A study of ~500 Japanese prostate cancer patients found that individuals with a rs351855(T;T) genotype had a 2.2- and 1.9-fold increased risk of prostate cancer and benign prostate hyperplasia (BPH), and a 1.8-fold increased risk of metastatic prostate cancer compared to the (C;C) genotype. A meta-analysis published in 2011, surveying a total of 2,618 cases of prostate cancer, concluded that the odds ratio per rs351855(T) allele was 1.17 (CI: 1.07...
normal risk
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rs1545985 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (G); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=6.6 x 10e-6, using an additive model of risk.
normal
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rs1056836, also known as 4326C/G, Val432Leu or L432V, is a SNP in the cytochrome P450 1B1 (CYP1B1) gene. This gene is a member of the CYP1 gene family and one of the major enzymes involved in the hydroxylation of estrogens, a reaction likely to be relevant in hormonal carcinogenesis. [In dbSNP orientation, the (C) allele encodes the Leu; the (G) the Val.] In a study of 153 Hispanic Caucasians with prostate cancer the rs1056836(G;G) genotype showed decreased risk compared to the more common (C;C) genotype (odds ratio = 0.31, p = 0.04, CI: 0.10-0.96). This report cites another study as indicating that rs1056836(C;C) high-risk stage III and IV breast cancer patients receiving dose-intense paclitaxel in combination with doxorubicin and cyclophosphamide experience a longer progression-free surv...
normal risk
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rs7652331 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (T); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=4.4 x 10e-5, using a dominant model of risk.
normal
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rs16260 (A) SNP located in the promoter region of the E-cadherin CDH1 gene is associated with increased risk of hereditary prostate cancer. The effect appears to be additive, in that compared to the rs16260(C;C) homozygotes, the rs16260(A;C) heterozygotes are at about a 1.5 - 1.7 fold increased risk, and the rs16260(A;A) homozygotes are at about a 2.6 fold increased risk. * see also OMIM 192090.0018 [OMIM:?]
common in clinvar
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rs1137100 is a nonsynonymous coding SNP in exon 4 of the leptin receptor LEPR gene. It has been reported to affect glucose tolerance and insulin response, and it is also one of five SNPs reported to be useful in a SNP set defining the risk of dying from prostate cancer among patients with the disease; see gs242 and gs243. [OMIM:LEPTIN RECEPTOR POLYMORPHISM]
normal risk This is the typical form, exhibiting normal risk for prostate cancer to learn more visit rs2987983
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In one large Swedish study, men with one or two rs2987983(C) alleles were reported to be at somewhat increased (odds ratio 1.22) risk for Prostate cancer compared to men homozygous for the wild type rs2987983(T) allele, however the risk can be reduced by adding phytoestrogens to the diet. [PharmGKB:Curated Haplotype tagging SNP.] [OMIM:ESTROGEN RECEPTOR 2; ESR2]
normal risk
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rs251177 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (C); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=0.000188, using an additive model of risk.
normal
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shows a significantly stronger association with more aggressive forms of prostate cancer (odds ratios (OR) = 1.15; P = 7.7 x 10(-9)). [PharmGKB:Curated GWAS Results: Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer (Initial Sample Size: 1,854 cases, 21,372 controls; Replication Sample Size: 8,239 cases, 7,590 controls; Risk Allele: rs721048-A).] [OMIM:EH DOMAIN-BINDING PROTEIN 1; EHBP1] [GWAS:Prostate cancer]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study (Initial Sample Size: 1,345 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Prostate cancer.] [GWAS:Prostate cancer]
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A study of ~1,800 Caucasian prostate cancer patients concludes that the rs2735839(A) allele is associated with aggressive prostate cancer in general, and more specifically, in Gleason score 7 patients, it is more often associated with being GS 4 + 3 rather than GS 3 + 4 (odd ratio 1.85, CI: 1.31-2.61). cancer-genetics these snps influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 Genotyping 13 SNPs (including this one) in 1,308 Caucasian prostate cancer patients led to the conclusion that while none of the SNP associations were as significant as having a first-degree family history of the disease, they did replicate. And in fact, for rs2735839,...
normal risk
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rs7017300 is one of 4 tightly linked SNPs in the 'locus 1' region of 8q24 chromosomal region, which has been linked in several studies to prostate cancer, initially through rs1447295. In a study of 1,563 patients of European ancestry, the odds ratio for prostate cancer associated with risk genotypes of locus 1 were reported as 1.70 (CI: 1.39-2.07). Two other regions of chromosome 8q24 were also studied.
Magnitude: 0
Frequency: 85.7%
Repute:Good
References:0
Frequency: 85.7%
Repute:Good
References:0
common in complete genomics
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rs11102001 is a potential candidate modifier of the effect of HCAs on prostate cancer risk.
normal
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rs1447295 is a SNP on chromosome 8q24, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs1447295 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs1447295(A;A) and (A;C) risk genotypes yield an odds ratio for developing prostate cancer of 1.22 (CI: 1.06-1.40, p=5.3x10-3) and may account for 5.4% of population attributable risk. The rs1447295] location could be responsible for about seven percent of prostate cancer cases in white men of north European descent. Thus, taken together with rs6983267, these two genetic changes could account for as much as one quarter of prostate cancer cases in white men. The increased risk was observed for all...
normal risk
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rs4242382 is one of 4 tightly linked SNPs in the 'locus 1' region of 8q24 chromosomal region, which has been linked in several studies to prostate cancer, initially through rs1447295. In a study of 1,563 patients of European ancestry, the odds ratio for prostate cancer associated with risk genotypes of locus 1 were reported as 1.70 (CI: 1.39-2.07). Two other regions of chromosome 8q24 were also studied. Genotyping 13 SNPs (including this one) in 1,308 Caucasian prostate cancer patients led to the conclusion that while none of the SNP associations were as significant as having a first-degree family history of the disease, they did replicate. In fact, for rs4242382, the risk estimate varied by family history. A joint-odds analysis indicates that rs4242382(A;A) individuals have increased pros...
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cancer-genetics these snps influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 [GWAS:Prostate cancer]
common in complete genomics
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rs10508266 and rs3750861 shows significant association with lung cancer risk rs3750861 affects expression of KLF6 splicing variants in prostate cancer and we found that its rare allele is associated with reduced lung cancer risk
Magnitude: 0
Frequency: 89.1%
References:22
Frequency: 89.1%
References:22
normal
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rs10090154 is a SNP in chromosome 8q24 'region 1', associated with increased risk for prostate cancer. The odds ratio for the (T) risk allele were 1.42 (CI: 1.07-1.87, p=0.014), and they were not significantly different between Caucasians and African-Americans in this study of ~500 patients. In follow-up studies looking at disease severity (and not just overall risk), this SNP is reported to account for the risk (from region 1) of advanced prostate cancer. Note that a meta-analysis across 10+ studies, including over 15,000 prostate cancer cases, reported the risk for a different SNP (rs1447295) representing the same region, 'region 1', of this chromosome. [OMIM:?] [GWAS:Prostate cancer]
Magnitude: 0
Frequency: 92.0%
Repute:Good
References:0
Frequency: 92.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 92.0%
Repute:Good
References:6
Frequency: 92.0%
Repute:Good
References:6
common in complete genomics
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According to a 23andMe report, the rs12621278(A;A) genotype is associated with 2.4 times higher risk of progression of prostate cancer. [GWAS:Prostate cancer]
Magnitude: 0
Frequency: 93.8%
References:1
Frequency: 93.8%
References:1
Magnitude: 0
Frequency: 93.8%
Repute:Good
References:52
Frequency: 93.8%
Repute:Good
References:52
normal risk
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rs16901979 is a SNP on chromosome 8q24, associated with increased risk for prostate cancer in several studies. In some studies, the regions have been divided, and this SNP falls in region 2. In a study of over 3,600 Caucasians with prostate cancer, rs16901979 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs16901979(A;A) and (A;C) risk genotypes yield an odds ratio for developing prostate cancer of 1.53 (CI: 1.22-1.92, p=1.8x10e-4) and may account for 3.6% of population attributable risk. cancer related according to this blog Two genetic markers in the 8q24 region of chromosome 8 rs7008482 and rs16901979 have been linked to an increased risk of prostate cancer in African Americans. abstract In follow-up studies looki...
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rs6983561 increases susceptibility to Prostate cancer 1.42 times for carriers of the C allele A common genetic risk factor for colorectal and prostate cancer. Confirmation study of prostate cancer risk variants at 8q24 in African Americans identifies a novel risk locus. 8q24 and prostate cancer: association with advanced disease and meta-analysis. Chromosome 8q24 markers: risk of early-onset and familial prostate cancer. Multiple independent genetic variants in the 8q24 region are associated with prostate cancer risk. Pooled analysis of genetic variation at chromosome 8q24 and colorectal neoplasia risk. Multiple loci with different cancer specificities within the 8q24 gene desert. Clinical utility of five genetic variants for predicting prostate cancer risk and mortality. Evaluation of 8q2...
common in complete genomics
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rs20415 and rs5270 prostate cancer Pyrosequencing of polymorphisms in the COX-2 gene (PTGS2) with reported clinical relevance.
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
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rs138213197, aka G84E, is a SNP in the homeobox transcription factor HOXB13 gene located in a cluster of HOX genes on ch 17q21–22. This gene is a member of the abdominal B subfamily, which have posterior domains of expression, including in the vertebrate urogenital system. HOXB13 maintains a relatively high level of expression in the adult prostate. G84E consists of the non-conservative replacement of a glutamic acid for a glycine at this position in the HOXB13 protein. In early 2012, findings were published based on exome sequencing of 200 genes spanning the ch17q21-22 region of primarily Caucasian prostate cancer patients (and matched controls). Deemed a 'rare but recurring mutation', rs138213197(T) was discovered and then validated in a larger case-case study. Overall, rs138213197...
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
common in clinvar
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This SNP, a variant in the CHEK2 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the risk (minor) allele is (C). rs17879961 one of 3 SNPs associated with increased risk of lung cancer [OMIM:?] [GWAS:Lung cancer]
normal
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The rs2740574(G) allele encodes a variant form of CYP3A4 known as CYP3A4*1B. rs2740574(G) alleles are associated with an ~10 fold higher risk of aggressive prostate cancer in African American males. [PMID 16414488, OMIM A pooled study (1,400+ samples) along with a replication study conducted by members of the Ovarian Cancer Association Consortium found a 2.5-2.8x increased risk for ovarian cancer] for rs2740574(G;G) individuals (CI: 1.2-6.5, p=0.017). The authors note that CYP3A4 encodes a key enzyme in estrogen metabolism and which may be linked to ovarian carcinogenesis. [PharmGKB:Curated Risk or phenotype-associated allele: CYP3A4*1B, rs2740574 G allele. Phenotype: CYP3A4*1B (rs2740574 G) allele carriers show a significantly increased risk for SCLC (OR = 2.25, p = 0.02), which showed a...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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rs78378222[C] (odds ratio (OR) = 2.36, P = 5.2 × 10?17). rs78378222 is in the 3? untranslated region of TP53 and changes the AATAAA polyadenylation signal to AATACA, resulting in impaired 3?-end processing of TP53 mRNA. Investigation of other tumor types identified associations of this SNP with prostate cancer (OR = 1.44, P = 2.4 × 10?6), glioma (OR = 2.35, P = 1.0 × 10?5) and colorectal adenoma (OR = 1.39, P = 1.6 × 10?4). However, we observed no effect for breast cancer, a common Li-Fraumeni syndrome tumor (OR = 1.06, P = 0.57, 95% confidence interval 0.88–1.27). [GWAS:Basal cell carcinoma]
114 snps
(hide) Pseudoxanthoma elasticum
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The ABCC6 rs2238472 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.006 Type of association: CO; TOX] [OMIM:PSEUDOXANTHOMA ELASTICUM]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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A spectrum of ABCC6 mutations is responsible for pseudoxanthoma elasticum. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Mutations in a gene encoding an ABC transporter cause pseudoxanthoma elasticum. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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[OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
16 snps
(hide) Psoriasis
1.5x increased risk for Crohn's disease; 2x increased risk for Graves' disease
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SNP rs2201841, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. Another study found that the 'A allele' and 'AA genotype' were significantly overrepresented in Graves' disease patients with Graves ophthalmopathy, based on 216 North American patients. The odds ratios reported were 2.04 for the allele (p=1x10<sup>-4</sup>), and for the so-called 'AA' genotype (presumably rs2201841(T;T) when correctly oriented to the dbSNP orientation), 2.4 (p=1x10<sup>-4</sup>). 23andMe blog psoriasis Europeans *rs2201841(G) 1.13x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication S...
1.43x increased risk of developing psoriasis and psoriatic arthritis
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IL12B gene SNP, part of a haplotype with rs6887695 associated with psoriasis. A study of 500+ patients with psoriatic arthritis (PsA) concluded that the odds ratio for rs3212227(A;A) carriers was 1.43 (CI: 1.17-1.76). The effect sizes observed in patients with PsA appear to be smaller than those previously reported in patients with psoriasis, suggesting that both loci are primarily associated with psoriasis susceptibility rather than primarily with psoriatic arthritis. rs568408 GA/AA and rs3212227 AC/CC variant genotypes were associated with a significantly increased risk of cervical cancer [adjusted odds ratio, 1.43; 95% confidence interval (CI), 1.06-1.93; and adjusted odds ratio, 1.30; 95% CI, 0.97-1.75, respectively]. subjects carrying variant genotypes of both loci had a 1.82-fold (95...
Magnitude: 1.1
Frequency: 91.8%
Repute:Bad
References:100
Frequency: 91.8%
Repute:Bad
References:100
Normal, but higher risk for certain autoimmune diseases. Almost everyone has this form, but it indicates a slightly higher risk of Ankylosing Spondylitis, Crohn's Disease (1.09x), Psoriasis (1.06x), and Ulcerative Colitis (1.06x). The risk is much greater than for the rare version. This is the interleukin-23 (IL-23) receptor. Media:http://www.the-rheumatologist.org/details/article/2528901/Neutralizing_IL-23_and_Its_Targets_May_Improve_Ankylosing_Spondylitis.html] Neutralizing IL-23 and Its Targets May Improve Ankylosing Spondylitis by Lara C. Pullen, PhD in The Rheumatologist newsmagazine ]
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A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-1....
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[PharmGKB:Non-Curated GWAS results: Identification of ZNF313/RNF114 as a novel psoriasis susceptibility gene (Initial Sample Size: 318 cases, 288 controls; Replication Sample Size: 2,361 cases, 1,927 controls). This variant is associated with Psoriasis.] [OMIM:?] [GWAS:None] [GWAS:Psoriasis]
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Source nature psoriasis rs887466(G) + rs4379333(C)
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23andMe blog psoriasis Europeans *rs610604(G) 1.19x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 6q23.3; Reported Gene(s): TNFAIP3; Risk Allele: rs610604-G); (p-value= 0.000000000009).This variant is associated with Psoriasis.] [GWAS:Psoriasis]
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rs7993214 was a significant SNP associated with risk for psoriasis in a large US/UK study. [PharmGKB:Non-Curated GWAS results: A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease Loci (Initial Sample Size: 218 cases, 519 controls; Replication Sample Size: 1,153 cases, 1,217 controls). This variant is associated with Psoriasis.] [GWAS:Psoriasis]
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rs4085613 is a SNP in the late cornified envelope 3D LCE3D gene cluster. rs4085613 has been associated with psoriasis in a Chinese study involving 1,139 cases and 1,132 controls. See also: 23andMe blog psoriasis Chinese *rs4085613(G) 1.32x risk [PharmGKB:Non-Curated GWAS results: Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. (Initial Sample Size: 1,139 Chinese cases, 1,132 Chinese controls; Replication Sample Size: 5,721 Chinese cases, 7,340 Chinese controls); (Region: 1q21.3; Reported Gene(s): LCE3D, LCE3A; Risk Allele: rs4085613-A); (p-value= 7E-30).This variant is associated with Psoriasis.] [OMIM:PSORIASIS SUSCEPTIBILITY 4; PSORS4]
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rs4112788 tags the LCE3C_LCE3B deletion that has been associated with risk for psoriasis in a study of 2,800+ samples of European ancestry. 23andMe blog psoriasis Europeans *rs4112788(G) 1.41x risk Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. Deletion of LCE3C and LCE3B genes at PSORS4 does not contribute to susceptibility to psoriatic arthritis in German patients. Genetic susceptibility to psoriasis: an emerging picture. Deletion of the late cornified envelope genes LCE3C and LCE3B is associated with psoriasis in a Chinese population. [PharmGKB:Curated This variant is a tagging SNP for LCE3C_LCE3B-del and is also strongly associated with psoriasis.] [OMIM:PSORIASIS SUSCEPTIBILITY 4; PSORS4] [GWAS:None]
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[PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 9q34.13; Reported Gene(s): TSC1; Risk Allele: rs1076160-T); (p-value= 0.000006).This variant is associated with Psoriasis.] [GWAS:Psoriasis]
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rs734232 has been reported in to be associated with psoriasis in a study of US psoriasis patients. However, the results of another study failed to support rs734232 as a psoriasis susceptibility factor in German psoriasis patients.
normal
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23andMe blog psoriasis Chinese *rs1265159(A) 22.62x risk Proxy SNP for rs1265181 Note that in dbSNP orientation, the risk allele for this SNP is rs1265159(T); also, see rs1265181 for more information.
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[PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 5q33.3; Reported Gene(s): IL12B; Risk Allele: rs2082412-G); (p-value= 2E-28).This variant is associated with Psoriasis.] [OMIM:PSORIASIS SUSCEPTIBILITY 11; PSORS11] [GWAS:Psoriasis]
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23andMe blog psoriasis Chinese *rs3213094(C) 1.28x risk [PharmGKB:Non-Curated GWAS results: Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. (Initial Sample Size: 1,139 Chinese cases, 1,132 Chinese controls; Replication Sample Size: 5,721 Chinese cases, 7,340 Chinese controls); (Region: 5q33.3; Reported Gene(s): IL12B; Risk Allele: rs3213094-A); (p-value= 3E-26).This variant is associated with Psoriasis.] [OMIM:PSORIASIS SUSCEPTIBILITY 11; PSORS11] [GWAS:Psoriasis]
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rs3803369 was a significant SNP associated with risk for psoriasis in a large US/UK study.
Frequency: 76.1%
References:6
References:6
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Genome-wide association scan yields new insights into the immunopathogenesis of psoriasis. Genetics of psoriasis and psoriatic arthritis. Psoriasis prediction from genome-wide SNP profiles. A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 6p21.33; Reported Gene(s): HLA-C; Risk Allele: rs12191877-T); (p-value= 1E-100).This variant is associated with Psoriasis.] [GWAS:Psoriasis]
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haplotype CCG (rs1184860, rs1167846, rs1167849) is significantly associated with psoriasis (OR 3.14, 95% CI 1.61-6.14), whereas the TTG haplotype had a protective effect (OR 0.20, 95% CI 0.07-0.55).
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rs20541 is a C/T polymorphism on the interleukin 13 gene IL13 associated with IgE levels. rs20541 influences the effect of maternal smoking during pregnancy and persistent childhood asthma rs1295685 and rs20541 were significantly associated with elevated IgE levels in pooled analyses. rs2569190(T;T) and rs2569191(C;C) genotypes associated with lower IgE 23andMe blog psoriasis Europeans rs20541(G) 1.27x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 5q31.1; Reported Gene(s): IL13; Risk Allele: rs20541-G); (p-value= 0.000000000000005).This variant is associated with Psoriasis.] [OMIM:PSORIASIS SUSCEP...
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rs4406273 is located about 28Kb centromeric of HLA-C on human chromosome 6, and as tested in at least three populations (from Europe, Pakistan and Thailand) it is an almost perfect (95%-99%) proxy for the HLA-C*06:02 MHC allele associated with psoriasis. The rs4406273(A) allele is the HLA-C*06:02 surrogate.
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rs628977 was associated with early-onset psoriasis in a study of 150 French adults. ADAM33, a new candidate for psoriasis susceptibility. ADAM33 genetic polymorphisms and risk of atopic dermatitis among Japanese children. ADAM33 genetic polymorphisms, smoking, and rhinoconjunctivitis in Japanese women: the Kyushu Okinawa Maternal and Child Health Study.
1.4x increased risk of psoriasis, psoriatic arthritis
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IL12B gene SNP, part of a haplotype with rs3212227 associated with psoriasis. rs6887695 confirmed to be associated with psoriasis in another study A study of 500+ patients with psoriatic arthritis (PsA) concluded that the odds ratio for rs6887695(G;G) carriers was 1.43 (CI: 1.18-1.74). The effect sizes observed in patients with PsA appear to be smaller than those previously reported in patients with psoriasis, suggesting that both loci are primarily associated with psoriasis susceptibility rather than primarily with psoriatic arthritis. [OMIM:INFLAMMATORY BOWEL DISEASE 19; IBD19] [GWAS:Crohn's disease]
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
Magnitude: 0
Frequency: 75.7%
Repute:Good
References:6
Frequency: 75.7%
Repute:Good
References:6
common
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rs10484554 was the most highly significant SNP associated with risk for psoriasis in a large US/UK study. rs10484554 was found to be associated with psoriasis based on a study by the eMERGE network in which electronic medical records were searched to find what clinical associations were associated with selected SNPs. Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study. New insights into the pathogenesis and genetics of psoriatic arthritis. Genome-wide association studies and the genetic dissection of complex traits. The search for host genetic factors of HIV/AIDS pathogenesis in the post-genome era: progress to date and new avenues for discovery. Genome-wide association study SNPs in the human genome diversi...
normal
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IL23R gene SNP, part of a haplotype with rs11209026 associated with psoriasis. In a study of 216 North American patients with Graves' disease, the homozygous rs10889677(T;T) genotype was significantly associated with Graves' disease but not specifically with Graves ophthalmopathy; the odds ratio was 9.4 (p=0.02).
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:7
Frequency: 85.8%
Repute:Good
References:7
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 5q33.1; Reported Gene(s): TNIP1; Risk Allele: rs17728338-A); (p-value= 1E-20).This variant is associated with Psoriasis.] [OMIM:PSORIASIS SUSCEPTIBILITY 11; PSORS11] [GWAS:Psoriasis]
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23andMe blog psoriasis Europeans *rs2066808(A) 1.34x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 12q13.2; Reported Gene(s): IL23A, STAT2; Risk Allele: rs2066808-A); (p-value= 0.000000001).This variant is associated with Psoriasis.] [GWAS:Psoriasis]
common The rs2395029(T;T) genotype is the common genotype for this SNP, against which the rs2395029(T;G) and rs2395029(G;G) genotypes that are associated with reduced HIV viral load in HIV carriers are compared. See also rs9264942 and HIV.
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rs2395029 is a SNP in the major histocompatibility complex (MHC) region, and several studies have shown that the rs2395029(G) allele is 99.9% predictive of the presence of an HLA-B*5701 allele. This HLA allele, in turn, has been associated with several conditions. A study of 51 cases of flucloxacillin drug-induced liver injury (DILI), an important cause of serious liver disease, along with a replication study of another 23 cases, found that the rs2395029(G) carriers were at highly increased risk (odds ratio 80, p=8.7x10(-33)). * see also: 23andMe blog rs2395029(G;G) increases the odds of drug-induced liver injury in response to flucloxacillin by 45x This SNP is thought to be involved in determining the HIV viral load set point during the asymptomatic period of infection. This SNP is estima...
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asthma related This SNP is in the promoter region of the IL-13 gene PMID: 17615386 IL-13 is involved in pulmonary inflammation, remodeling and susceptibility to chronic obstructive pulmonary disease (COPD). This IL13 promoter polymorphism may modulate the adverse effects of cigarette smoking on pulmonary function in long-term cigarette smokers. Every 20 pack-year increment in smoking was associated with a 2.4% reduction in mean ppFEV1(forced expiratory volume in 1 second, a measure used to assess lung disease, like COPD) in the common homozygous (CC) or heterozygous (CT) promoter genotypes, and an 8.2% reduction in mean ppFEV1 in minor allele homozygotes (TT, recessive model). *pack-year= packs per day x years smoked rs1800925 and/or rs11568506 related to psoriasis and/or Crohn's disease ?...
complex; generally normal risk
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rs361525 is also known as the TNF-238 SNP, and occasionally the rs361525(A) allele is referred to as 238.2 (with the more common (G) allele being 238.1). This SNP in the tumor necrosis factor-alpha gene has been linked to a wide variety of conditions: * Breast cancer ** A large study of over 5,000 Caucasian women found that rs361525(A) allele carriers were at somewhat elevated risk for breast cancer compared to the (G;G) genotype, with an odds ratio per allele of 1.18, CI: 1.04-1.35, p(trend)= 0.008. ** However, a 2009 European study of 30,000 breast cancer cases, compared to 30,000 controls, found no association, or as they put it, 'persuasive evidence against an overall association between invasive breast cancer risk and (this SNP)'. * Graft versus host disease (GVHD) ** A study of ~100 ...
normal
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rs1265181 is a SNP in the HLA region of chromosome 6. A large study (>6,000 Chinese psoriasis patients and an equal number of controls) found a highly significant association between the minor rs1265181(G) allele and risk for psoriasis. A proxy for this allele is rs1265159(A). See also: 23andMe blog psoriasis [PharmGKB:Non-Curated GWAS results: Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. (Initial Sample Size: 1,139 Chinese cases, 1,132 Chinese controls; Replication Sample Size: 5,721 Chinese cases, 7,340 Chinese controls); (Region: 6p21.33; Reported Gene(s): MHC; Risk Allele: rs1265181-?); (p-value= NS).This variant is associated with Psoriasis.] [GWAS:Psoriasis]
30 snps
(hide) Psoriatic arthritis
1.43x increased risk of developing psoriasis and psoriatic arthritis
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IL12B gene SNP, part of a haplotype with rs6887695 associated with psoriasis. A study of 500+ patients with psoriatic arthritis (PsA) concluded that the odds ratio for rs3212227(A;A) carriers was 1.43 (CI: 1.17-1.76). The effect sizes observed in patients with PsA appear to be smaller than those previously reported in patients with psoriasis, suggesting that both loci are primarily associated with psoriasis susceptibility rather than primarily with psoriatic arthritis. rs568408 GA/AA and rs3212227 AC/CC variant genotypes were associated with a significantly increased risk of cervical cancer [adjusted odds ratio, 1.43; 95% confidence interval (CI), 1.06-1.93; and adjusted odds ratio, 1.30; 95% CI, 0.97-1.75, respectively]. subjects carrying variant genotypes of both loci had a 1.82-fold (95...
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[GWAS:Celiac disease]
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23andMe blog psoriasis Europeans *rs610604(G) 1.19x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 6q23.3; Reported Gene(s): TNFAIP3; Risk Allele: rs610604-G); (p-value= 0.000000000009).This variant is associated with Psoriasis.] [GWAS:Psoriasis]
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A US study of 1,172 lymphoma patients and 982 controls looked at 57 SNPs in 36 immune function genes. Five SNPs in two cytokine genes, tumor necrosis factor-alpha and lymphotoxin-alpha, were associated with a 1.31x increase in non-Hodgkin lymphoma (OR, 1.31; 95% CI, 1.06-1.63; P = 0.01) and with a 1.64x increase in the subtype known as diffuse large B cell lymphoma (OR, 1.64; 95% CI, 1.23-2.19; P = 0.0007). The other four SNPS are listed below. The cytokine genes affect inflammatory and innate immune responses. * rs1800629 * rs361525 * rs1799724 * rs2239704 [PharmGKB:Curated Risk or phenotype-associated allele, tested allele: unspecified; minor allele designation varies by ethnicity in dbSNP Phenotype: In 114 cases and 414 controls (n = 528), univariate analysis of disease association sho...
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[GWAS:None]
Frequency: 52.7%
References:2
References:2
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http://blog.23andme.com/2012/03/02/snpwatch-new-genetic-insight-into-the-causes-of-eczema/ linked to eczema
Frequency: 86.7%
References:0
References:0
1.4x increased risk of psoriasis, psoriatic arthritis
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IL12B gene SNP, part of a haplotype with rs3212227 associated with psoriasis. rs6887695 confirmed to be associated with psoriasis in another study A study of 500+ patients with psoriatic arthritis (PsA) concluded that the odds ratio for rs6887695(G;G) carriers was 1.43 (CI: 1.18-1.74). The effect sizes observed in patients with PsA appear to be smaller than those previously reported in patients with psoriasis, suggesting that both loci are primarily associated with psoriasis susceptibility rather than primarily with psoriatic arthritis. [OMIM:INFLAMMATORY BOWEL DISEASE 19; IBD19] [GWAS:Crohn's disease]
normal/common in clinvar
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reports rs4795067, with risk/non-risk alleles G/A, has an odds ratio of 1.2 (p=2e−7) for psoriatic arthritis based on a case/control study of ~2,000 patients. Nitric oxide synthase genes and their interactions with environmental factors in Parkinson's disease. Lead exposure, polymorphisms in genes related to oxidative stress, and risk of adult brain tumors. [GWAS:None]
Magnitude: 0
Frequency: 67.3%
Repute:Good
References:1
Frequency: 67.3%
Repute:Good
References:1
common on affy axiom data
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Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. [GWAS:Celiac disease]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
common on affy axiom data
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reports rs33980500, with risk/non-risk alleles T/C, has an odds ratio of 1.6 (p=2.65e−16) for psoriatic arthritis based on a case/control study of ~2,000 patients. [GWAS:None]
19 snps
(hide) Resting heart rate
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[GWAS:Resting heart rate]
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rs365990 is a nonsynonymous SNP in exon 25 of the ''MYH6'' gene, coding for the alpha myosin heavy chain (alpha-MyHC) protein. The A->G nucleotide change results in the A1101V missense mutation in alpha-MyHc. [rs365990 was discovered in a study conducted by deCODE Genetics as being most significantly associated primarily with heart rate, but also with PR interval. In the Icelandic cohort of ~10,000 individuals in the discovery phase and an additional ~10,000 individuals in the follow-up phase, the rs365990 G allele frequency was 0.34, and the G allele was associated with decreased heart rate (p=9.4E-11 for both phases combined) and with a prolonged PR interval (p=1.8E-5 combined). After adjusting for heart rate, the association of rs365990 with PR interval maintained significance (p=0.0...
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A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. Genetic determinants of circulating sphingolipid concentrations in European populations. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. A single nucleotide polymorphism in the FADS1/FADS2 gene is associated with plasma lipid profiles in two genetically similar Asian ethnic groups with distinctive differences in lifestyle. Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC). Genetic variation in lipid desaturases and its impact on the development of human disease. Genetic loci associated with lipid concentrations and cardi...
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[GWAS:Resting heart rate]
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[GWAS:Resting heart rate]
5 snps
(hide) Restless legs syndrome
1.44x increased risk of developing restless legs syndrome
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rs4626664, a SNP in the motor neuron PTPRD gene, has been linked to restless legs syndrome based on a study of several European populations totaling ~2,500 patients. The odds ratio associated with the rs4626664(A) risk allele is 1.44 (CI: 1.31-1.59, adjusted p = 5 x 10e-10). Note that a nearby SNP, rs1975197, was also shown to independently confer risk for restless legs syndrome in this same study. Restless Legs Syndrome: Preliminary Research [PharmGKB:Curated GWAS Results: PTPRD (protein tyrosine phosphatase receptor type delta) is associated with restless legs syndrome (Initial Sample Size: 628 cases, 1,644 controls; Replication Sample Size: 1,835 cases, 3,111 controls; Risk Allele: rs4626664-A). This variant is associated with Restless legs syndrome.] [OMIM:RESTLESS LEGS SYNDROME, SUSC...
1.3x increased risk of developing restless legs syndrome
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rs1975197, a SNP in the motor neuron PTPRD gene, has been linked to restless legs syndrome based on a study of several European populations totaling ~2,500 patients. The odds ratio associated with the rs1975197(T) risk allele is 1.31 (CI: 1.20-1.44, adjusted p = 5 x10e-9). Note that a nearby SNP, rs4626664, was also shown to independently confer risk for restless legs syndrome in this same study. Restless Legs Syndrome: Preliminary Research [PharmGKB:Curated GWAS Results: PTPRD (protein tyrosine phosphatase receptor type delta) is associated with restless legs syndrome (Initial Sample Size: 628 cases, 1,644 controls; Replication Sample Size: 1,835 cases, 3,111 controls; Risk Allele: rs1975197-T). This variant is associated with Restless legs syndrome.] [OMIM:RESTLESS LEGS SYNDROME, SUSCEP...
1.7x risk for developing restless legs syndrome Variants in MEIS1 rs2300478, BTBD9 rs9357271, and MAP2K5/SKOR1 rs1026732 confer a significant risk of RLS in a US population. Association studies of variants in MEIS1, BTBD9, and MAP2K5/SKOR1 with restless legs syndrome in a US population.
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rs2300478, a SNP located in the MEIS1 gene, has been linked to restless legs syndrome, a common sleep disorder, with an overall odds ratio of 1.78 (CI: 1.52-2.09) for the (G) risk allele . The association between this SNP and RLS has been replicated in three European populations, within family lines but not in sporadic cases . The highest association to restless legs syndrome is a haplotype consisting of the rs6710341(A) and rs12469063(G) alleles. This haplotype gives rise to an odds ratio of 2.75 (CI: 2.23-3.41) . Variants in MEIS1 rs2300478, BTBD9 rs9357271, and MAP2K5/SKOR1 rs1026732 confer a significant risk of RLS in a US population. In another study, rs2300478 was not associated with attention deficit hyperactivity disorder (ADHD). Association studies of variants in MEIS1, BTBD9, and...
Slightly increased risk of developing restless legs syndrome rs3923809 is a A/G variation on human chromosome 6. Associated with: Restless legs syndrome. This SNP, located in an intron of the BTBD9 gene, has a variant that is seen somewhat more frequently in individuals with restless legs syndrome. The risk allele is rs3923809(A); carriers of two such alleles, i.e. those with rs3923809(A;A) genotypes, are estimated to be 1.9 fold more likely to have restless legs syndrome than rs3923809(G;G) individuals. The authors of this study suggest that perhaps half of the cases of restless legs syndrome may involve the rs3923809 risk genotypes. Consistent with this finding, another report about rs3923809 links the (G) minor allele to a lower frequency of restless legs syndrome with an overall odds ...
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This SNP, located in an intron of the BTBD9 gene, has a variant that is seen somewhat more frequently in individuals with restless legs syndrome. The risk allele is rs3923809(A); carriers of two such alleles, i.e. those with rs3923809(A;A) genotypes, are estimated to be 1.9 fold more likely to have restless legs syndrome than rs3923809(G;G) individuals. The authors of this study suggest that perhaps half of the cases of restless legs syndrome may involve the rs3923809 risk genotypes. Consistent with this finding, another report about rs3923809 links the (G) minor allele to a lower frequency of restless legs syndrome with an overall odds ratio of 0.57 (CI: 0.48-0.68). Note that 70-80% of all individuals in European populations carry one or two copies of the (A) major allele, yet restless le...
0.69x risk risk of developing restless legs syndrome
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rs4489954, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.69 (CI: 0.69-0.82) for the (T) minor allele. [PharmGKB:Curated In replicated GWAS case-control studies of Caucasian(European and French-Canadian) familial and sporadic RLS, the G allele of rs4489954 was significantly associated with Restless Legs Syndrome.]
0.71x risk of developing restless legs syndrome
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rs3784709, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.71 (CI: 0.60-0.83) for the (T) minor allele. [PharmGKB:Curated In replicated GWAS case-control studies of Caucasian(European and French-Canadian) familial and sporadic RLS, the C allele of rs3784709 was significantly associated with Restless Legs Syndrome.]
0.70x risk for restless legs
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rs1026732, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.70 (CI: 0.59-0.82) for the (A) minor allele. [PharmGKB:Curated In replicated GWAS case-control studies of Caucasian(European and French-Canadian) familial and sporadic RLS, the G allele of rs1026732 was significantly associated with Restless Legs Syndrome.]
Magnitude: 1.5
Frequency: 48.7%
Repute:Good
References:3
Frequency: 48.7%
Repute:Good
References:3
0.70x risk for restless legs
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rs11635424, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.70 (CI: 0.59-0.82) for the (A) minor allele. [PharmGKB:Curated In replicated GWAS case-control studies of Caucasian(European and French-Canadian) familial and sporadic RLS, the G allele of rs11635424 was significantly associated with Restless Legs Syndrome.]
Magnitude: 1.5
Frequency: 50.0%
Repute:Good
References:6
Frequency: 50.0%
Repute:Good
References:6
0.71x risk for restless legs
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rs12593813, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.71 (CI: 0.60-0.83) for the (A) minor allele. Restless Legs Syndrome: Preliminary Research [PharmGKB:Curated GWAS Results: Genome-wide association study of restless legs syndrome identifies common variants in three genomic regions (Initial Sample Size: 401 cases, 1,644 controls; Replication Sample Size: 1,158 cases, 1,178 controls; Risk Allele: rs12593813-G).] [GWAS:None] [GWAS:Restless legs syndrome]
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Restless Legs Syndrome: Preliminary Research
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association with restless leg syndrome
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Restless Legs Syndrome: Preliminary Research
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association with restless leg syndrome
0.71x risk for restless legs
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rs6494696, a SNP located in a region of chromosome 15q, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.71 (CI: 0.60-0.83) for the (C) minor allele. The association between this SNP and RLS has been replicated in three European populations. [PharmGKB:Curated In replicated GWAS case-control studies of Caucasian(European and French-Canadian) familial and sporadic RLS, the G allele of rs6494696 was significantly associated with Restless Legs Syndrome.] [OMIM:RESTLESS LEGS SYNDROME, SUSCEPTIBILITY TO, 1]
Normal risk of developing restless legs syndrome
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rs9357271, a SNP located in the BTBD9 gene region, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.63 (CI: 0.52-0.75) for the (C) minor allele. This SNP may also be associated with Tourette syndrome (TS), particularly TS without obsessive-compulsive disorder, based on a study of ~600 patients. [PharmGKB:Curated In replicated GWAS case-control studies of Caucasian(European and French-Canadian) familial and sporadic RLS, the T allele of rs9357271 was significantly associated with Restless Legs Syndrome.] [OMIM:RESTLESS LEGS SYNDROME, SUSCEPTIBILITY TO, 6] [GWAS:None]
common
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rs9296249, a SNP located in the BTBD9 gene region, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.62 (CI: 0.52-0.75) for the (C) minor allele. [PharmGKB:Curated GWAS Results: Genome-wide association study of restless legs syndrome identifies common variants in three genomic regions (Initial Sample Size: 401 cases, 1,644 controls; Replication Sample Size: 1,158 cases, 1,178 controls; Risk Allele: rs9296249-T).] [OMIM:RESTLESS LEGS SYNDROME, SUSCEPTIBILITY TO, 6] [GWAS:Restless legs syndrome]
16 snps
(hide) Retinitis pigmentosa
References:6
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
5 snps
(hide) Rheumatoid Arthritis
increased risk for celiac disease increased resistance to bacterial infections
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rs3184504 is a nonsynonymous SNP in the SH2B3 gene, and it is also known as R262W. In a recent (2008) study of non-HLA SNP associations of 1600+ celiac disease patients, this SNP was considered one of the most significant. The odds ratio for the minor allele was 1.19 (CI:1.10-1.30, p=1.33x10e-7). rs653178, another SNP in strong linkage disequilibrium (r<sup>2</sup>>0.99) with rs3184504, was also associated with celiac disease. associated with type-1 diabetes 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 23andMe blog blood pressure Pharmacogenetic implications for eight common blood pressure-associated...
3.6x increased risk of sexual dysfunction when taking SSRI Antidepressants. Selective Seratonin Reuptake Inhibitors (citalopram (Celexa), escitalopram (Lexapro), fluoxetine (Prozac), paroxetine (Paxil), or sertraline (Zoloft)) cause worse sexual dysfunction (a common side-effect) in people with this SNP. Note that research has shown Saffron is effective at reversing the sexual dysfunction from SSRI anti-depressants.
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
1.2x risk Rheumatoid Arthritis
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rs6920220 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.20 (CI 1.06-1.36), and for homozygotes, 1.72 (CI 1.33-2.22). rheumatoid arthritis *rs6920220 [P= 2.6 x 10(-6), OR 1.22 (1.13-1.33)]. *rs5029937 *rs13207033 protective [P= 0.0001, OR 0.86 (0.8-0.93)] perfectly correlated with rs10499194 The combination of the carriage of both risk alleles of rs6920220 and rs5029937 together with the absence of the protective allele of rs13207033 was strongly associated with RA when compared to carriage of none [OR of 1.86 (95% CI) (1.51-2.29)]. This equates to an effect size of 1.50 (95% CI 1.21-1.85) Lack of association or interactions between the IL-4, IL-4Ralpha an...
1.94x risk of developing rheumatoid arthritis
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rs3738919, a SNP located in the ITGAV gene, was identified in a European study to be associated with rheumatoid arthritis (RA). The risk allele for rs3738919 is the more common allele, (C). For the three European Caucasian populations studied (372 RA patients + 330 controls), and combining the (C;C) and (A;C) genotypes in comparison to the (A;A) genotype, the odds ratio for RA = 1.94 (CI: 1.3–2.9, p = 0.002). There was no significant difference in RA risk between those carrying one or two (C) alleles. An editorial about this finding has been published.
1.32 x risk of rheumatoid arthritis. A common genetic variant at the TRAF1-C5 locus on chromosome 9 is associated with an increased risk of anti-CCP-positive rheumatoid arthritis. rs3761847, a SNP located between two genes associated with chronic inflammation (TRAF1 and C5), is associated with increased risk of anti CCP-positive rheumatoid arthritis. The risk allele is (G); the odds ratio reported is 1.32 (95% confidence interval, 1.23 to 1.42; P=4x10-14) .
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rs3761847, a SNP located between two genes associated with chronic inflammation (TRAF1 and C5), is associated with increased risk of anti CCP-positive rheumatoid arthritis. The risk allele is (G); the odds ratio reported is 1.32 (95% confidence interval, 1.23 to 1.42; P=4x10-14) . rs3761847(G;G) associated with an increased risk of death (hazard ratio 3.96 [95% confidence interval 1.24-12.6], P = 0.020) as compared with (A;A) homozygote status. The excess mortality was attributed to deaths due to malignancies and sepsis but not cardiovascular disease (CVD). [PharmGKB:Non-Curated GWAS Results: TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study (Initial Sample Size: 1,493 cases, 1,831 controls; Replication Sample Size: 1,053 cases, 1,858 controls; Risk Allele: rs3761847-G...
Magnitude: 2
Frequency: 21.2%
Repute:Bad
References:29
Frequency: 21.2%
Repute:Bad
References:29
2x increased risk of developing SLE; 1.6x increased risk of developing primary biliary cirrhosis; and 1.7x increased risk of developing Sjögren's syndrome
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rs10488631, a SNP located 3' of the IRF5 gene, has been reported as a possibly causative SNP for systemic lupus erthymatosus (SLE), based on a study of ~700 Swedish patients. The risk allele is rs10488631(C), with a reported odds ratio of 2.07 (CI: 1.63-2.62, p = 9x10e-10). The C allele is also associated with primary biliary cirrhosis, with each C increasing the odds about 1.6 times. Each C allele increases risk of Sjögren's syndrome by 1.7 times. SLE rs10488631 and rs7582694 [OMIM:INTERFERON REGULATORY FACTOR 5; IRF5] [GWAS:Systemic lupus erythematosus]
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
complex; generally greater risk for cancer progression
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rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and H131R. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...
1.4x increased risk of SLE
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The rs2004640(A) allele had a higher frequency in SLE cases (0.385) than controls (0.321; odds ratio (OR) = 1.32, P = 0.0003). In combined analysis, including all seven independent cohorts from the three studies so far, robust and consistent associations of the rs2004640(A) allele with SLE were observed. The estimate of risk was OR = 1.44 (CI: 1.34-1.55), with an overall P = 1.85 x 10(-23) for the rs2004640(A) allele. The haplotype (rs2004640T-rs2280714A) involved in both the alternative splice donor site and the elevated expression of IRF5 also had a highly significant association with SLE (pooled, P = 2.11 x 10(-16)). Our results indicate that the genetic effect on the risk of SLE mediated by IRF5 variants can be generally accepted in both white and Asian populations. A meta-analysis com...
Slightly increased risk for multiple autoimmune diseases, such as type-1 diabetes Higher risk of type-1 diabetes.
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rs763361, also known as Gly307Ser, is a SNP in the immune response CD226 gene. The rs763361(T) allele (in dbSNP orientation) encodes the Ser. Based on multiple studies (by one group) now totaling over 2,000 patients, the rs763361(T) allele is associated with increased risk for multiple autoimmune diseases, including type-1 diabetes (p = 3 x 10e-9), multiple sclerosis (p = 4 x 10e-4), and possibly rheumatoid arthritis (p = 0.017). Based on tag SNP analysis, the authors conclude that this SNP could be the causal variant. Tested in a large multiple sclerosis data set consisting of 2369 trio families, 5737 cases and 10 296 unrelated controls, SNP rs763361 was associated with disease risk (p = 5.4 x 10e-8) [PharmGKB:Non-Curated GWAS Results: Robust associations of four new chromosome regions f...
increased risk for auto-immune diseases
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The rs3087243 SNP is also known in the literature as the CT60 G>A or the +6230G>A polymorphism, and it is located in the CTLA4 gene. In Asian (Japanese) populations, the presence of an rs3087243(G) allele represents a 1.3 fold increased risk of autoimmune thyroid disease, and for those with autoimmune thyroid disease, a 1.5 fold increased risk of type-1 diabetes. However, in individuals without autoimmune thyroid disease, no association was seen between this SNP and type-1 diabetes. The authors speculate that earlier studies may have reported associations between this SNP and type-1 diabetes that were actually primarily based on the association with autoimmune thyroid disease. This same SNP, rs3087243, has also been implicated as a (minor) risk factor for developing rheumatoid arthri...
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[GWAS:Rheumatoid arthritis]
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One of 42 more SNPs associated with rheumatoid arthritis based on a meta-analysis of 30,000 patients, most with odds ratios of 1.01 - 1.2. [GWAS:Rheumatoid arthritis]
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Based on a study of 400 Spanish patients with rheumatoid arthritis, SNP rs1324913 in the KLF12 gene was significantly associated with increased risk, showing even higher association than the rs2476601 SNP located in the PTPN22 gene. A SNP said to be perfectly correlated with rs1324913 is rs9565072; this latter SNP failed to show any association with rheumatoid arthritis in a UK cohort of 3962 cases and 3531 controls, and also failed in a meta-analysis of UK, US and Swedish populations.
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A SNP said to be perfectly correlated with rs1324913 is rs9565072; this latter SNP failed to show any association with rheumatoid arthritis in a UK cohort of 3962 cases and 3531 controls, and also failed in a meta-analysis of UK, US and Swedish populations.
1.8x increased risk for rheumatoid arthritis
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Two SNPs on ch 1q in the CD244 gene, rs3766379 and rs6682654, were found to be associated with risk for rheumatoid arthritis in two independent Japanese cohorts (p = 3.23 x 10e-8) and p = 7.45 x 10e-8). The odds ratio reported for the more common rs6682654(G) allele, as oriented in dbSNP and not the publication, was 1.34 (CI: 1.15-1.55, p = 0.0002). [OMIM:RHEUMATOID ARTHRITIS; RA]
1.9x increased risk for rheumatoid arthritis
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Two SNPs on ch 1q in the CD244 gene, rs3766379 and rs6682654, were found to be associated with risk for rheumatoid arthritis in two independent Japanese cohorts (p = 3.23 x 10e-8) and p = 7.45 x 10e-8). The odds ratio reported for the more common rs3766379(T) allele was 1.37 (CI: 1.18-1.59, p = 0.0001). [OMIM:CD244 ANTIGEN; CD244]
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One of 42 more SNPs associated with rheumatoid arthritis based on a meta-analysis of 30,000 patients, most with odds ratios of 1.01 - 1.2. [GWAS:Hodgkin's lymphoma]
1.3x risk
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rs9550642 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.34 (CI 1.15-1.56), and for homozygotes, 2.23 (CI 1.21-4.13).
1.3x risk
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rs3816587 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 0.91 (CI 0.80-1.04), and for homozygotes, 1.35 (CI 1.14-1.59). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,860 cases, 2,938 controls; Replication Sample Size: NR; Risk Allele: rs3816587-C). This variant is associated with rheumatoid arthritis.] [GWAS:Rheumatoid arthritis]
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[OMIM:?] [GWAS:Rheumatoid arthritis]
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[GWAS:Rheumatoid arthritis]
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[OMIM:?] [GWAS:Rheumatoid arthritis]
Frequency: 20.4%
References:1
References:1
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[GWAS:Rheumatoid arthritis]
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[GWAS:None]
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[GWAS:Rheumatoid arthritis]
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rs4728142, rs3807306 and a 5 bp insertion-deletion linked multiple sclerosis in three populations Associated with systemic lupus erythematosus (SLE) in African Americans. [OMIM:INTERFERON REGULATORY FACTOR 5; IRF5] [GWAS:Rheumatoid arthritis]
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One of 42 more SNPs associated with rheumatoid arthritis based on a meta-analysis of 30,000 patients, most with odds ratios of 1.01 - 1.2. [GWAS:Rheumatoid arthritis]
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One of 42 more SNPs associated with rheumatoid arthritis based on a meta-analysis of 30,000 patients, most with odds ratios of 1.01 - 1.2. [GWAS:None]
higher risk for RA
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rs6313, also known as T102C, is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6313(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs1328674 in dbSNP is opposite that cited by this publication; therefore, with respect to dbSNP, the haplotype of risk as cited above is CACC rather than CTCC. see also gs108 and gs226 Polymorphisms in the serotonin receptor gene HTR2A are associated with quantitative traits in panic disorder. [PharmGKB:Curated Risk or phenotype-associated allele (s): T/T. Phenotype: Patients, with a diagnosis of probable Alzheimer's disease, carryi...
Frequency: 29.2%
References:1
References:1
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[GWAS:Rheumatoid arthritis]
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[GWAS:Type 1 diabetes]
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[GWAS:Rheumatoid arthritis]
Frequency: 32.3%
References:28
References:28
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rs10499194 associated with rheumatoid arthritis In a concurrent study, the Wellcome Trust Case Control Consortium (WTCCC) has reported strong association of rheumatoid arthritis susceptibility to a different SNP located 3.8 kb from rs10499194 (rs6920220; P = 5 x 10(-6) in WTCCC). We show that these two SNP associations are statistically independent, are each reproducible in the comparison of our data and WTCCC data, and define risk and protective haplotypes for rheumatoid arthritis at 6q23. rheumatoid arthritis *rs6920220 [P= 2.6 x 10(-6), OR 1.22 (1.13-1.33)]. *rs5029937 *rs13207033 protective [P= 0.0001, OR 0.86 (0.8-0.93)] perfectly correlated with rs10499194 The combination of the carriage of both risk alleles of rs6920220 and rs5029937 together with the absence of the protective allel...
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rs2240335 is in linkage disequilibrium with a polymorphism that increases susceptibility to Rheumatoid Arthritis 1.75 times for carriers of the G allele [GWAS:None]
average
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Several studies have all found that rs2240340, a SNP in the PADI4 gene, is associated with risk for developing rheumatoid arthritis (RA). The risk allele in dbSNP orientation is (T). The largest study involved over 2,000 RA patients, and although implicating PTPN22 SNPs with greater risk, PADI4 SNP rs2240340 was also implicated. The odds ratio varied between the two (European) populations a bit, but when combined, was 1.10 (CI: 1.00 - 1.21) for the risk allele. Additional studies include: rs2240340 was modestly associated with rheumatoid arthritisin a study of 950 unrelated Japanese subjects with RA, with an odds ratio of 1.22 (CI: 1.04 - 1.43,p=0.012). rs2240340 was associated with rheumatoid arthritis with an odds ratio of 1.97 (CI: 1.44 – 2.69), based on 830 cases and...
Frequency: 37.2%
References:8
References:8
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[OMIM:?] [GWAS:Rheumatoid arthritis]
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[GWAS:Rheumatoid arthritis]
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[OMIM:?] [GWAS:Rheumatoid arthritis]
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[GWAS:Rheumatoid arthritis]
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rs2301888 increases susceptibility to Rheumatoid Arthritis 1.82 times for carriers of the C allele [GWAS:Rheumatoid arthritis]
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[GWAS:Rheumatoid arthritis]
1.2x risk
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rs6684865 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.27 (CI 1.02-1.56), and for homozygotes, 1.54 (CI 1.25-1.90).
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[PharmGKB:Non-Curated GWAS Results: Common variants at CD40 and other loci confer risk of rheumatoid arthritis (Initial Sample Size: 3,393 cases, 12,460 controls; Replication Sample Size: 3,929 cases, 5,807 controls; Risk Allele: rs3890745-T). This variant is associated with Rheumatoid arthritis.] [OMIM:RHEUMATOID ARTHRITIS; RA] [GWAS:Rheumatoid arthritis] [GWAS:Rheumatoid arthritis]
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[GWAS:Rheumatoid arthritis]
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One of 42 more SNPs associated with rheumatoid arthritis based on a meta-analysis of 30,000 patients, most with odds ratios of 1.01 - 1.2. [GWAS:Rheumatoid arthritis]
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[GWAS:Rheumatoid arthritis]
Frequency: 42.9%
References:1
References:1
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[GWAS:Rheumatoid arthritis]
Frequency: 44.2%
References:2
References:2
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rs11761231 has been reported in a large study to be associated with rheumatoid arthritis, particularly in females. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.44 (CI 1.19-1.75), and for homozygotes, 1.64 (CI 1.35-1.99). The association between rs11761231 and rheumatoid arthritis did not reproduce in a North American population, emphasizing 'the need to carefully account for population structure to avoid false-positive disease associations'. Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Rheumatoid arthritis susceptibility loci at chromosomes 10p15, 12q13 and 22q13. Association of common polymorphisms in known susceptibility genes with rheumatoid arthritis in a Slovak population using osteo...
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rs1748035 is in linkage disequilibrium with a polymorphism that increases susceptibility to Rheumatoid Arthritis 1.09 times for heterozygotes (AG) and 1.10 times for homozygotes (AA) rs1748035 is in linkage disequilibrium with a polymorphism that increases susceptibility to Rheumatoid Arthritis 1.20 times for heterozygotes (AG) and 1.68 times for homozygotes (AA) rs1748035 is in linkage disequilibrium with a polymorphism that increases susceptibility to Rheumatoid Arthritis 2.00 times for carriers of the A allele
Frequency: 45.1%
References:6
References:6
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[GWAS:Type 1 diabetes]
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A large-scale rheumatoid arthritis genetic study identifies association at chromosome 9q33.2. Adjusting for HLA-DRbeta1 in a genome-wide association analysis of rheumatoid arthritis and related biomarkers. Replication of recently identified associated single-nucleotide polymorphisms from six autoimmune diseases in Genetic Analysis Workshop 16 rheumatoid arthritis data. Armitage's trend test for genome-wide association analysis: one-sided or two-sided? A genome-wide association scan for rheumatoid arthritis data by Hotelling's T2 tests. Allelic based gene-gene interactions in rheumatoid arthritis. Comparative analysis of different approaches for dealing with candidate regions in the context of a genome-wide association study. [GWAS:Rheumatoid arthritis]
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One of 42 more SNPs associated with rheumatoid arthritis based on a meta-analysis of 30,000 patients, most with odds ratios of 1.01 - 1.2. [GWAS:Rheumatoid arthritis]
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rs1930780 is in linkage disequilibrium with a polymorphism that increases susceptibility to Rheumatoid Arthritis 1.36 times for heterozygotes (CG) and 1.52 times for homozygotes (CC)
Normal risk of developing rheumatoid arthritis
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A variant located 64 bp upstream of the first untranslated exon (exon 1A), consisting of a 5 bp insertion/deletion CGGGG, may be the causative SNP in this region that is most responsible for increasing SLE risk, however it lacks an rs# (i.e. it isn't registered in dbSNP). A meta-analysis comprising 5 case-control studies, totaling 6,582 rheumatoid arthritis cases and 5,375 controls, concluded that several IRF5 gene SNPs were indeed (still) significantly associated with the disease. The rs729302(C) allele was associated with a slight protective effect (odds ratio 0.89, CI: 0.8-0.977, p = 0.015). [GWAS:Systemic lupus erythematosus]
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rs743777 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.09 (CI 0.97-1.24), and for homozygotes, 1.72 (CI 1.40-2.11). Lack of association or interactions between the IL-4, IL-4Ralpha and IL-13 genes, and rheumatoid arthritis. Rheumatoid arthritis susceptibility loci at chromosomes 10p15, 12q13 and 22q13. Representation of genetic association via attributable familial relative risks in order to identify polymorphisms functionally relevant to rheumatoid arthritis. AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm. A novel galectin-1 and interleukin 2 receptor beta haplotype is associate...
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[GWAS:Rheumatoid arthritis]
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Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations. Association of CD40 with rheumatoid arthritis confirmed in a large UK case-control study. Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis. Genetic variants in the prediction of rheumatoid arthritis. Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment. Endometriosis and autoimmune disease: association of susceptibility to moderate/severe endometriosis with CCL21 and HLA-DRB1. [PharmGKB:Non-Curated GWAS Results: Common variants at CD40 and other loci confer risk of rheumatoid arthritis (Initial Sample Size: 3,393 cases, 12,460 controls; Replic...
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[GWAS:Rheumatoid arthritis]
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[OMIM:?] [GWAS:Rheumatoid arthritis]
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Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. Assessing the reproducibility of asthma candidate gene associations, using genome-wide data. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [OMIM:INFLAMMATORY BOWEL DISEASE 22; IBD22] [GWAS:Crohn's disease]
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[GWAS:Rheumatoid arthritis]
Frequency: 52.3%
References:1
References:1
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[GWAS:Rheumatoid arthritis]
Frequency: 53.8%
Repute:Bad
References:21
Repute:Bad
References:21
1.4x increased risk for rheumatoid arthritis
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rs10818488, a SNP located in between the C5 and TRAF1 genes, was identified as the SNP from this region showing maximal association with rheumatoid arthritis in a study of ~2000 Dutch, Swedish, and American patients. This study also reported that this SNP was significantly (p = 0.008) associated with increased disease progression as determined by radiographic damage over time in rheumatoid arthritis patients. The risk allele for rs10818488 is the minor allele, (A). If (and as) reported from just the Dutch RA patients, the odds ratio associated with rs10818488(A;G) heterozygotes is 1.38 (CI 1.04-1.83, p = 0.027) and with rs10818488(A;A) homozygotes 2.06 (95% CI 1.42-2.98, p = 1.29E-3). Combining data from all 2,000 patients, the odds ratio associated with rs10818488(A) is 1.26 (CI 1.15-1.37...
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[GWAS:Rheumatoid arthritis]
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[GWAS:Rheumatoid arthritis]
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rs4810485 is a SNP associated with rheumatoid arthritis (RA), a chronic autoimmune disease characterized by joint inflammation. At this locus, the minor allele, T, protects against RA. The SNP is located on chromosome 20q13 in the second intron of the CD40 gene, which encodes a receptor that is expressed on the surface of multiple immune cells. CD40 binds the ligand CD154 which is expressed by activated T cells, and this interaction plays a critical role in T cell helper activity in the immune system. rs4810495 is closely linked with another SNP, rs1883832, that appears to lesson translation of the CD40 gene, affecting this critical signaling pathway that leads to B cell proliferation . Mouse model knockouts of CD40 have been shown to alleviate arthritis . The association between rs4810485...
Frequency: 55.8%
References:11
References:11
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[GWAS:Rheumatoid arthritis]
1.9x increased risk for SLE (lupus)
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rs3748079 is a SNP in the promoter region of the ITPR3 gene; it is also known as -1990C>T. rs3748079 has been linked to increased risk for systemic lupus erythematosus (SLE) in two independent Japanese case-control samples (p=0.0000000178 with odds ratio of 1.88, CI:1.51-2.35). Individuals with risk genotypes of both rs3748079 and rs3095870, in the ITPR3 and NKX2.5 genes, respectively, have even high risk for SLE (odds ratio 5.77). This particular SNP also revealed associations with rheumatoid arthritis (RA) (p=0.0084 with odds ratio of 1.23, CI:1.05-1.43) and with Graves' disease (GD) (p=0.00036 with odds ratio of 1.57, CI:1.22-2.02). Note that the orientation of this SNP as published is reversed compared to the dbSNP entry. [OMIM:SYSTEMIC LUPUS ERYTHEMATOSUS; SLE]
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rs2442728 is a SNP located in the MHC region, upstream of HLA-B and about 1.2 Mb telomeric of DRB1. A study of 855 rheumatoid arthritis patients concluded that rs2442728 was one of only two SNPs representing an additional susceptibility gene - in addition to HLA-DRB1 - within the MHC region.
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[PharmGKB:Non-Curated GWAS Results: Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility (Initial Sample Size: 400 cases, 400 controls; Replication Sample Size: 410 cases, 394 controls; Risk Allele: rs2002842-A). This variant is associated with Rheumatoid arthritis.] [GWAS:Rheumatoid arthritis]
normal risk of rheumatoid arthritis, SLE, Sjögren's syndrome, type-1 diabetes, and primary biliary cirrhosis.
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune dise...
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rs7026551 increases susceptibility to Rheumatoid Arthritis 1.31 times for carriers of the C allele
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[GWAS:Rheumatoid arthritis]
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rs1343125, a SNP in the MAGI3 gene, was associated with rheumatoid arthritis.
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rs4678 is a SNP representing an Arg/Gln variation in the VARS2L gene. A study of 855 rheumatoid arthritis patients concluded that rs4678 was one of only two SNPs representing an additional susceptibility gene - in addition to HLA-DRB1 - within the MHC region. There is some inconsistency in this SNP. The reference assembly considers it a A/G while RefSNP calls it a C/T.
Frequency: 67.7%
References:11
References:11
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Association of STAT4 with rheumatoid arthritis in the Korean population. Re-evaluation of putative rheumatoid arthritis susceptibility genes in the post-genome wide association study era and hypothesis of a key pathway underlying susceptibility. Specificity of the STAT4 genetic association for severe disease manifestations of systemic lupus erythematosus. A risk haplotype of STAT4 for systemic lupus erythematosus is over-expressed, correlates with anti-dsDNA and shows additive effects with two risk alleles of IRF5. Role of STAT4 polymorphisms in systemic lupus erythematosus in a Japanese population: a case-control association study of the STAT1-STAT4 region. Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis. Evidence for STAT4 as a common aut...
normal for RA; 1.4x increased GD risk
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rs3789604 is associated with increased susceptibility to rheumatoid arthritis, based on a study of ~1,000 Caucasian individuals. The odds ratio is 1.55x for (G;T) heterozygotes and 1.73x for (G;G) homozygotes. However, in a Japanese population, the other allele, rs3789604(T), is associated with increased risk (odds ratio 1.45, p=0.0085) for Graves' disease (GD). [OMIM:?]
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[PharmGKB:Non-Curated Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample Size: 6,225 cases, 6,946 controls, 3,064 trios); (Region: 10p15.1; Reported Gene: PRKCQ; Risk Allele: rs947474-G) This variant is associated with Type 1 diabetes.] [OMIM:DIABETES MELLITUS, INSULIN-DEPENDENT; IDDM] [GWAS:Type 1 diabetes]
Frequency: 74.3%
References:2
References:2
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[GWAS:Rheumatoid arthritis]
Frequency: 78.8%
References:14
References:14
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Of SNPs outside the HLA region, this SNP and one other (rs6822844) in the region of the IL21 gene showed the strongest association with celiac disease in a study of ~800 Caucasian patients and a meta-analysis of two further populations. [OMIM:KIAA1109 GENE; KIAA1109] [GWAS:Rheumatoid arthritis]
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[GWAS:Rheumatoid arthritis]
Frequency: 86.7%
Repute:Bad
References:2
Repute:Bad
References:2
2x risk
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rs11162922 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.27 (CI 0.41-4.01), and for homozygotes, 2.00 (CI 0.64-6.20).
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rs7528684 rs3792876 and rs2268277 failed to showed a statistically significant association with rheumatoid arthritis rs2268277, a SNP in the RUNX1 gene, has been associated in a Japanese population with rheumatoid arthritis at at odds ratio of 1.28 (CI = 1.10–1.48). The study involved 719 cases and 441 controls.
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An ambiguous flip whose risk allele could not be determined from the original data Risk alleles for multiple sclerosis identified by a genomewide study. PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm. An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. Genetic variants in the HLA-DRB1 gene are associated with Kashin-Beck disease in the Tibetan population. [GWAS:Rheumatoid arthritis]
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[GWAS:Rheumatoid arthritis]
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[PharmGKB:Curated GWAS Results: Common variants at CD40 and other loci confer risk of rheumatoid arthritis (Initial Sample Size: 3,393 cases, 12,460 controls; Replication Sample Size: 3,929 cases, 5,807 controls; Risk Allele: rs1678542-C). This variant is associated with Rheumatoid arthritis.] [OMIM:RHEUMATOID ARTHRITIS; RA] [GWAS:Rheumatoid arthritis] [GWAS:Rheumatoid arthritis]
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Association of CD40 with rheumatoid arthritis confirmed in a large UK case-control study. Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis. Genetic variants in the prediction of rheumatoid arthritis. [PharmGKB:Non-Curated GWAS Results: Common variants at CD40 and other loci confer risk of rheumatoid arthritis (Initial Sample Size: 3,393 cases, 12,460 controls; Replication Sample Size: 3,929 cases, 5,807 controls; Risk Allele: rs42041-G). This variant is associated with Rheumatoid arthritis.] [GWAS:Rheumatoid arthritis]
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Representation of genetic association via attributable familial relative risks in order to identify polymorphisms functionally relevant to rheumatoid arthritis. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.
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Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis. Genetic variants in the prediction of rheumatoid arthritis. Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment. [PharmGKB:Curated This SNP located on chromosomes 10p15 is associated with susceptibility to rheumatoid arthritis in a validation study of 4,106 individuals with rheumatoid arthritis and an expanded reference group of 11,238 subjects.] [GWAS:Rheumatoid arthritis]
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
normal
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rs6457617 has been reported in a large study to be associated with rheumatoid arthritis. This SNP is reported to be the most statistically significant of many SNPs similarly located in the MHC region. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 2.36 (CI 1.97-2.84), and for homozygotes, 5.21 (CI 4.31-6.30). [GWAS:Rheumatoid arthritis]
normal risk
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rs1343151 is one of several SNPs in the IL23R gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.8 (p=1.0x10e-5). rs1343151 with rheumatoid arthritis (OR=1.14 [1.06-1.22], P=4x10-4) rs1343151 was '''not''' associated with rheumatoid arthritis in a study of 1,200+ Korean patients. A;A homozygous individuals showed a strongly reduced risk of Crohn's Disease compared those who were G;G homozygous. [PharmGKB:Non-Curated GWAS results: Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci (Initial Sample Size: 382 trios; Replication Sample Size: 521 trios, 750 cases, 828 controls). This variant is associated with Crohn's disease. This v...
normal
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This SNP, along with SNPs rs6910071 and rs3817964, is a tag SNP for the HLA-DRB1*0401 allele. The HLA-DRB1*0401 allele has been associated with higher risk for rheumatoid arthritis, and in particular, rheumatoid vasculitis. The association is seen particularly for individuals carrying two copies of, i.e. homozygous for, the allele. The reported odds ratio for rs660895(G;G) homozygotes is 6.2 (CI: 1.01 - 37.9). The risk for rheumatoid arthritis may be higher for individuals carrying one copy (one 'dose') of the HLA-DRB1*0401 allele, if they also carry a different HLA-DRB1 risk allele. In particular, *0401/*0404 individuals are reported to have an odds ratio for rheumatoid vasculitis of 4.1 (CI: 1.1 - 16.2), and *0401/*0101 individuals have an odds ratio of 4.0 (CI: 1.4 - 11.6). *(A;A) is 0 ...
normal
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rs7528684 has been reported to be associated with rheumatoid arthritis in a Caucasian population, following reports of a similar association in a Japanese population. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 0.95 (CI 0.83-1.08), and for homozygotes, 2.30 (CI 1.64-3.23). In a study of 645 Caucasians from Southern Spain with multiple sclerosis, the rs7528684(G) allele (in dbSNP orientation) was found to be somewhat protective (per allele odds ratio 0.81, CI: 0.70-0.94, p=0.007). In another report , a summary indicates the following regarding disease and odds ratio (OR)for rs7528684: * for rheumatoid arthritis: OR = 2.15 (CI = 1.58–2.93), from 830 cases and 658 controls; * for SLE: OR = 1.49 (CI = 1.16â€...
normal
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This SNP, along with SNPs rs660895 and rs3817964, is a tag SNP for the HLA-DRB1*0401 allele. The HLA-DRB1*0401 allele has been associated with higher risk for rheumatoid arthritis, and in particular, rheumatoid vasculitis. The association is seen particularly for individuals carrying two copies of, i.e. homozygous for, the allele. The reported odds ratio for rs6910071(G;G) homozygotes is 6.2 (CI: 1.01 - 37.9). The risk for rheumatoid arthritis may be higher for individuals carrying one copy (one 'dose') of the HLA-DRB1*0401 allele, if they also carry a different HLA-DRB1 risk allele. In particular, *0401/*0404 individuals are reported to have an odds ratio for rheumatoid vasculitis of 4.1 (CI: 1.1 - 16.2), and *0401/*0101 individuals have an odds ratio of 4.0 (CI: 1.4 - 11.6). rs6910071 wa...
1.7x risk for RA; 1.6X for T1D; also MS?
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rs2104286 has also been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.30 (CI 1.02-1.65), and for homozygotes, 1.57 (CI 1.25-1.99). The same (A) allele of rs2104286, which is located in the first intron of the IL2RA gene, was calculated to confer a slight increase (19%) in the risk of developing multiple sclerosis. [PMID tbd; NEJM 357, 29 July 2007, DA Hafler et al.] Note that the (A) allele is the most common at this position in all known populations. blog post giving perspective on the significance of this SNP with respect to multiple sclerosis news announcement rs2104286 was significantly associated with UK cases of juvenile idiopathic arthritis (JIA)(allelic odds ra...
normal
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rs2269475 is a SNP in the allograft inflammatory factor-1 (AIF-1) gene, which may be involved in inflammatory processes. In a study of 276 Polish Caucasian patients with rheumatoid arthritis, the frequency of rs2269475(A) carriers among patients was 31.9% vs 19.1% among controls (p = 0.0003). The frequency of individuals positive for anti-cyclic citrullinated peptide (anti-CCP) antibodies was also significantly elevated in these carriers (odds ratio 8.82, CI: 2.06-37.7). Allograft inflammatory factor-1 and tumor necrosis factor single nucleotide polymorphisms in systemic sclerosis. An allograft inflammatory factor 1 (AIF1) single nucleotide polymorphism (SNP) is associated with anticentromere antibody positive systemic sclerosis.
normal
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rs2837960 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 0.95 (CI 0.83-1.08), and for homozygotes, 2.30 (CI 1.64-3.23). Rheumatoid arthritis susceptibility loci at chromosomes 10p15, 12q13 and 22q13. Representation of genetic association via attributable familial relative risks in order to identify polymorphisms functionally relevant to rheumatoid arthritis. AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm. [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,860 cases, 2,938 contr...
common on affy axiom data
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association with rheumatoid arthritis and type-1 diabetes point to a general risk locus for autoimmune diseases. Also, of SNPs outside the HLA region, this SNP and one other (rs13119723) in the region of the IL21 gene showed the strongest association with celiac disease in a study of ~800 Caucasian patients and a meta-analysis of two further populations. A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci. Association study of IL2/IL21 and FcgRIIa: significant association with the IL2/IL21 region in Scandinavian coeliac disease families. Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Gene variants influencing mea...
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
normal
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rs6679677 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.98 (CI 1.72-2.27), and for homozygotes, 3.32 (CI 1.93-5.69). rs6679677 was also reported in the same study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.82 (CI 1.59-2.09), and for homozygotes, 5.19 (CI 3.15-8.55). Recently (Feb 2008), it has been asserted that the association between rs6679677 and type-1 diabetes is actually completely due to a closely linked, potentially causal variant identified as rs2476601, which is also known as Arg620Trp. In this study, apparently the largest to date, the odds ratio...
Magnitude: 0
Frequency: 82.3%
Repute:Good
References:0
Frequency: 82.3%
Repute:Good
References:0
common in complete genomics
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rs10985112 increases susceptibility to Rheumatoid Arthritis 1.57 times for carriers of the A allele Genome-wide association study of rheumatoid arthritis by a score test based on wavelet transformation.
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rs2073838 and rs3792876 replicated for rheumatoid arthritis in Japanese, but not Caucasian populations. [PharmGKB:Curated In a replication study in a Japanese population and a metaanalysis of 9 studies confirmed an association of this SNP in the SLC22A4 gene with rheumatoid arthritis in Japanese population. The associations in Caucasian studies were not significant.]
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NOTE: information for rs1050152 was accidentally entered for this SNP, rs3792876. Although the SNPs are in the same gene, the original reference does not specifically refer to rs3792876 and the degree of linkage has not been confirmed. rs1051052, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T). A nearby SNP in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. rs2073838 and rs3792876 replicated for rheumatoid arthritis in Japanese, but not Caucasian populations. rs3792876 faile...
Magnitude: 0
Frequency: 83.2%
Repute:Good
References:2
Frequency: 83.2%
Repute:Good
References:2
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[GWAS:Rheumatoid arthritis]
higher risk for RA
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rs6314, also known as C1354T or His452Tyr/H452Y, is a SNP in the serotonin 2A receptor HTR2A gene. Based on a study of 166 Caucasian patients being treated for depression with paroxetine, rs6314 heterozygotes were associated with better response. There was a significantly higher frequency of heterozygotes in the remitter and response groups in comparison to the non-remitter (odds ratio 7.50, p=0.002) and non-response groups (odds ratio 5.25, p=0.01). * rs6314 is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6314(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs13286...
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rheumatoid arthritis *rs6920220 [P= 2.6 x 10(-6), OR 1.22 (1.13-1.33)]. *rs5029937 *rs13207033 protective [P= 0.0001, OR 0.86 (0.8-0.93)] perfectly correlated with rs10499194 The combination of the carriage of both risk alleles of rs6920220 and rs5029937 together with the absence of the protective allele of rs13207033 was strongly associated with RA when compared to carriage of none [OR of 1.86 (95% CI) (1.51-2.29)]. This equates to an effect size of 1.50 (95% CI 1.21-1.85) [OMIM:?]
common in complete genomics
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Meta-analysis found 1.4x risk of rheumatoid arthritis for rs2230926(G;G) An association was found between Systemic lupus erythematosus (SLE) and rs2230926. Three independent SNPs in the TNFAIP3 region (rs13192841, rs2230926 and rs6922466) are associated with systemic lupus erythematosus (SLE) among individuals of European ancestry. Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. Meta-analysis and imputation identifies a 109 kb risk haplotype spanning TNFAIP3 associated with lupus nephritis and hematologic manifestations. Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23. Complex genetic association of 6q23 with autoimmune rh...
normal risk
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A common SNP only in Asian populations, this SNP (also known as 1425G/A) and a close neighbor also in the PRKCH gene, rs3783799, have been associated with higher risk for subcortical silent brain infarction, a common form of stroke. In one study of ~1100 Japanese stroke patients, the odds ratio for carriers of the rs2230500(A) risk allele was reported as 1.40 (CI: 1.23-1.59, p=5x10e-7). A subsequent study reported the odds ratio for carriers of the (A) allele as 1.27 (CI: 1.09-1.48, p=0.0026) compared to individuals homozygous for rs2230500(G), based on studies of ~300 Japanese patients. rs2230500 (V374I) and rs9943582 were significantly associated with stroke Genetic association between the PRKCH gene encoding protein kinase Ceta isozyme and rheumatoid arthritis in the Japanese population...
normal
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This SNP, along with SNPs rs6910071 and rs660895, is a tag SNP for the HLA-DRB1*0401 allele. The HLA-DRB1*0401 allele has been associated with higher risk for rheumatoid arthritis, and in particular, rheumatoid vasculitis. The association is seen particularly for individuals carrying two copies of, i.e. homozygous for, the allele. The reported odds ratio for rs3817964(T;T) homozygotes is 6.2 (CI: 1.01 - 37.9). The risk for rheumatoid arthritis may be higher for individuals carrying one copy (one 'dose') of the HLA-DRB1*0401 allele, if they also carry a different HLA-DRB1 risk allele. In particular, *0401/*0404 individuals are reported to have an odds ratio for rheumatoid vasculitis of 4.1 (CI: 1.1 - 16.2), and *0401/*0101 individuals have an odds ratio of 4.0 (CI: 1.4 - 11.6).
116 snps
(hide) Rhizomelic chondrodysplasia punctata type 1
common in clinvar
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rs1805137, also known as L292X, is a mutation in the peroxisome targeting signal 2 receptor PEX7 gene. This mutation, if inherited in two copies or with another defective PEX7 allele, is considered causative for Rhizomelic chondrodysplasia punctata type 1. This SNP is also called i3002517 and i6055953 by 23andMe. [OMIM:?]
common in clinvar
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rs61753238, also known as Tyr40Ter or Y40X, is a mutation in the PEX7 gene on chromosome 6. The rare variant rs61753238(G) allele leads to the autosomal recessive disorder Rhizomelic chondrodysplasia punctata type 1 disorder when inherited in two copies or in compound heterozygotes. [OMIM:?]
4 snps
(hide) Salla disease
normal
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https://www.23andme.com/you/journal/salla/techreport/ Salla disease rs80338794
1 snp
(hide) Sarcoidosis
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[GWAS:Sarcoidosis]
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Crohn's disease and sarcoidosis 1,317 patients (660 CD and 657 SA) and 1,091 controls. rs1398024(A) odds ratio of 0.81 (95% confidence interval [CI], 0.69-0.96) [PharmGKB:Non-Curated GWAS Results: Genome-wide association study anaylsis in sarcoidosis and Crohn disease unravels a common susceptibility locus on 10p12.2 (Initial Sample Size: 382 CD cases, 398 SA cases, 394 controls; Replication Sample Size: 660 CD cases, 657 SA cases, 1,091 controls; Risk Allele: rs1398024-A). This variant is associated with Sarcoidosis and Crohn disease.] [GWAS:Crohn's disease and Sarcoidosis (combined)]
normal
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rs1049550, also known as R230C, is a SNP in the annexin A11 ANXA11 gene. 499 German individuals with sarcoidosis and 490 controls; Validation in an independent sample 1,649 cases, 1,832 controls. rs2789679: P = 3.0 x 10(-13), rs7091565: P = 1.0 x 10(-5)rs1049550, T > C, R230C was found to be strongly associated with sarcoidosis. rs2789679 P = 3.0 x 10(-13), rs7091565: P = 1.0 x 10(-5), allele-based test). Extensive fine mapping located the association signal to a region between exon 5 and exon 14 of ANXA11. A common nonsynonymous SNP (rs1049550, T > C, R230C) was found to be strongly associated with sarcoidosis Note that several ANXA11 SNPs are all tightly linked: rs1953600, rs2573346, rs2784773 and rs1049550. [PharmGKB:Curated A genome-wide association study in 499 German individua...
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
5 snps
(hide) Schizophrenia
3.7x higher risk for schizophrenia
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rs2270641 is a SNP in the vesicular monoamine transporter SLC18A1 gene, encoding a Thr4Pro substitution. In dbSNP orientation, the (G) allele is associated with the Proline. A study of 62 patients with schizophrenia concluded that the frequency of rs2270641(G;G) homozygotes was significantly higher. The reported odds ratio was 3.74 (CI: 1.7-8.2, p=0.0006) in this population of European descent. Note: another SNP, rs56575139, marks the same genomic location as rs2270641.
some risk linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil).
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
Increased risk of mental disorders
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rs16944 is a SNP in the interleukin 1, beta gene, a member of the cytokine family involved in the inflammatory response. The rs16944 G;G genotype is associated with risk for multiple mental illnesses. An increased risk for schizophrenia was found in a genetic association study of 2111 Caucasian individuals with an odds ratio of 1.24 (95% CI 1.09, 1.41) . Studies examining the brains of schizophrenic and bipolar individuals found reduced gray matter and hypoactivity associated with the G;G genotype. Additionally, this genotype is associated with impaired ability to achieve remission in a study of 256 Caucasian individuals with depression (odds ratio = 1.74; 95% confidence interval 1.2-4.3). The rs16944 A allele increases susceptibility to Osteoarthritis, with 1.80 times for heterozygotes (A...
Normal (higher) risk of Asthma.
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rs4950928 in CHI3L1 is likely to play roles in the predisposition to schizophrenia. An attempt to repeat the association between rs4950928 and risk for schizophrenia in an ethnically identical population (Japanese) as well as a new population (Han Chinese) failed to show any significant association. In contrast to previous studies, in this study of 6514 Danish adults the rs4950928(G) allele - rather than the (C) allele - was found to be associated with asthma. [PharmGKB:Non-Curated GWAS Results: Effect of Variation in CHI31 on Serum YKL-40 Level, Risk of Asthma, and Lung Function (Initial Sample Size: 632 individuals; Replication Sample Size: 206 children; Risk Allele: rs4950928-G). This variant is associated with YKL-40 levels.] [OMIM:CHITINASE 3-LIKE 1; CHI3L1] [GWAS:YKL-40 levels]
Magnitude: 1.5
Frequency: 28.3%
Repute:Bad
References:3
Frequency: 28.3%
Repute:Bad
References:3
Slightly higher risk for basal cell carcinoma
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rs12210050 was found to be associated with basal cell carcinoma based on a study by the eMERGE network in which electronic medical records were searched to find clinical associations associated with selected SNPs. [GWAS:Tanning]
increased risk of schizophrenia in limited study
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Associated with schizophrenia in a study of Croatians. Due to the limited number and diversity of the studied population, more study is needed to confirm any link. The G allele was associated with an increased risk of schizophrenia.
increased risk of schizophrenia in limited study
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Associated with schizophrenia in a study of Croatians. Due to the limited number and diversity of the studied population, more study is needed to confirm any link. The T allele was associated with an increased risk of schizophrenia. A network of dopaminergic gene variations implicated as risk factors for schizophrenia. Family based association study of pediatric bipolar disorder and the dopamine transporter gene (SLC6A3). Genome-wide and candidate gene association study of cigarette smoking behaviors. Financial and psychological risk attitudes associated with two single nucleotide polymorphisms in the nicotine receptor (CHRNA4) gene. Two loci control tuberculin skin test reactivity in an area hyperendemic for tuberculosis.
1.58x increased schizophrenia risk for women
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A total of 2,274 cases of schizophrenia were studied, resulting in an association between rs7341475, exclusively in women. Based on all populations the estimated relative risk for women carrying the common (G;G) genotype is 1.58 (p = 8.8 x 10(<sup>-7</sup>). This finding was replicated in a large independent Ashkenazi Jewish collection (721 cases, 259 female; 1455 controls, 834 female), with confirmation that it applies to both schizophrenia and schizoaffective disorder. [PharmGKB:Non-Curated GWAS results: Genome-Wide Association Identifies a Common Variant in the Reelin Gene That Increases the Risk of Schizophrenia Only in Women. (Initial Sample Size: 660 cases, 2,271 controls; Replication Sample Size: 2,274 cases, 4,401 controls); (Region: 7q22.1; Reported Gene(s): RELN; Ris...
Magnitude: 1.5
Repute:Bad
References:1
Repute:Bad
References:1
>2x higher risk for schizophrenia
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In the Pseudoautosomal region rs28694718, located in intron 8 of the CSF2RA gene, is part of a haplotype block that has been reported in a whole genome association study to be associated with schizophrenia. (The other SNP in this block is rs28414810.) The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with this allele is 2.11.
1.4x increased risk for schizophrenia
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23andMe blog schizophrenia *rs3131296(C) increased the odds of schizophrenia by 1.19x *rs12807809(T) increased the odds of schizophrenia by 1.15x *rs9960767(C) increased the odds of schizophrenia by 1.23 times. A study of ~2,500 Han Chinese patients with schizophrenia did find rs3131296 to be significantly associated in this population. [GWAS:Schizophrenia]
1.3x higher risk for schizophrenia (among Han Chinese)
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rs2024513 is a SNP in the neurexin-1 NRXN1 gene on chromosome 2p16.3. Based on a case-control study of 700+ Han Chinese patients with schizophrenia, rs2024513(A) was associated with higher risk, at an odds ratio of 1.3 (CI: 1.07 - 1.56, p=0.006).
1.1x increased risk for schizophrenia
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rs1344706 is a SNP in the ZNF804A gene, and it is probably the first SNP to have been reported as achieving genome-wide significance for psychosis. Reviews the literature, and concludes that rs1344706 is 'robustly, if modestly' associated with increased risk for schizophrenia. A genome-wide association study of schizophrenia (479 cases, 2,937 controls) followed by additional testing and a meta-analysis concluded that the strongest evidence for association was around ZNF804A (rs1344706; p = 1.61 x 10e-7) and that the finding was strengthened when the affected phenotype included bipolar disorder (p = 9.96 x 10e-9). Executive function, neural circuitry, and genetic mechanisms in schizophrenia. Apoptotic engulfment pathway and schizophrenia. Persistence criteria for susceptibility genes for sc...
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Genetic variation in the serotonin 2A receptor and suicidal ideation in a sample of 270 Irish high-density schizophrenia families.
Frequency: 8.0%
References:3
References:3
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rs11098403 is an intergenic SNP on chromosome 4 located ~300kb upstream of the 5' end of the NDST3 gene. Although in one publication the rs11098403(G) allele is said to be associated with increased risk for schizophrenia (odds ratio of 1.4, at least in Ashkenazi Jews), in another report this same allele is associated with decreased risk (odds ratio 0.6, in Han Chinese).,
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Association between rs2799573 and psychiatric disorders was shown in a 2013 study by the Cross-Disorder Group of the Psychiatric Genomics Consortium . In this study, genome-wide SNP data consisting of 1,250,922 autosomal SNPs were analyzed to identify genetic variants associated with autism spectrum disorder, ADHD, bipolar disorder, major depressive disorder, and schizophrenia. 33,332 cases and 27,888 controls included both unrelated and family-based samples (trios). A multinomial logistic regression procedure was used to identify the best-fitting model of relations between genotype and phenotype. This SNP, on chromosome 10 in an intron of CACNB2, was one of four genome-wide significant signals associated with the five psychiatric disorders (p = 4.29 x 10-8). The risk allele T exhibited al...
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haplotype less common in schizophrenia rs2273206(T), rs2273207(G), rs2228480(G).
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[GWAS:Schizophrenia]
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[GWAS:Schizophrenia]
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Bipolar I disorder and schizophrenia: a 440-single-nucleotide polymorphism screen of 64 candidate genes among Ashkenazi Jewish case-parent trios. RGS4 mRNA expression in postmortem human cortex is associated with COMT Val158Met genotype and COMT enzyme activity. RGS4 is not a susceptibility gene for schizophrenia in Japanese: association study in a large case-control population. Association of RGS2 and RGS5 variants with schizophrenia symptom severity. Interaction between interleukin 3 and dystrobrevin-binding protein 1 in schizophrenia. Association of RGS4 variants with schizotypy and cognitive endophenotypes at the population level. A genome-wide investigation of SNPs and CNVs in schizophrenia. [PharmGKB:Curated This variant is associated with differential antipsychotic treatment respon...
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linked to schizophrenia with rs7598440, rs839523, and rs707284 [OMIM:V-ERB-B2 AVIAN ERYTHROBLASTIC LEUKEMIA VIRAL ONCOGENE HOMOLOG 4; ERBB4]
Frequency: 19.5%
References:1
References:1
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[GWAS:Schizophrenia]
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haplotype less common in schizophrenia rs2273206(T), rs2273207(G), rs2228480(G). [PharmGKB:Curated Risk or phenotype-associated allele: not available in abstract. Phenotype: Positive association between rs2228480 SNP and thyroglobulin levels in thyroid cancer. Study size: 106 cases and 302 controls. Study population/ethnicity: Thyroid cancer patients and healthy individuals. Significance metric(s): not available in abstract. Type of association: CO; GN.]
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: 'Haplotype association analysis suggests that the haplotype CCGCA (at SNPs rs3125, rs6314, rs1923886, rs2224721 and rs2770296) is protective against bipolar disorder (P = 0.021, odds ratio 0.63) and the rarer haplotype CCACG confers risk to the disorder (P = 0.0065, odds ratio 3.08).' Genetic variation in the serotonin 2A receptor and suicidal ideation in a sample of 270 Irish high-density schizophrenia families.
Frequency: 21.4%
References:1
References:1
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[GWAS:Schizophrenia]
Magnitude: 1
Frequency: 23.0%
Repute:Bad
References:3
Frequency: 23.0%
Repute:Bad
References:3
increased risk of schizophrenia in limited study
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Associated with schizophrenia in a study of Croatians. Due to the limited number and diversity of the studied population, more study is needed to confirm any link. The C allele was associated with an decreased risk of schizophrenia. [PharmGKB:Curated This variant along with 3 other SNPs near DRD4 (4 SNP haplotype: rs3758653; rs916457; rs762502; rs11246226) is associated with tardive dyskinesia in male schizophrenia patients.]
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rs211105, rs1800532 and rs7933505 related to schizophrenia [OMIM:TRYPTOPHAN HYDROXYLASE 1; TPH1]
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rs795009 and rs310762 have been linked to schizophrenia [OMIM:SYNAPSIN II; SYN2]
Frequency: 25.9%
References:8
References:8
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schizophrenia *375 case and 812 control subjects *rs10399805 p = .018 and rs2275351; p = .008. An attempt to repeat the association between rs10399805 and risk for schizophrenia in an ethnically identical population (Japanese) as well as a new population (Han Chinese) failed to show any significant association. rs10399805(T;T) genotype showed a 2.5-fold increase in CHI3L1 mRNA expression in peripheral blood cells than those with (C;C) which is associated with the risk of atopy. [PharmGKB:Curated In a sample of 375 case and 812 control subjects a significant association of schizophrenia with this SNP (rs10399805) in the promoter region of CHI3L1 was identified. The variant is located at position -247 and disrupts the C/EBP-AML-1 binding site in the gene promoter. The risk allele is predict...
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schizophrenia the SNPs (rs1049623, rs2267641 and rs2239518) haplotype remaining significant even after adjustment for multiple testing (adjusted P=0.0136).
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A recent study in a Japanese population found that each C allele at rs833497 in the DYM gene is associated with 1.16x higher odds of schizophrenia. Defects in the DYM gene are also associated with Dyggve-Melchior-Clausen syndrome, an extremely rare disease found mostly among families with Lebanese or Spanish ancestry.
normal
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rs1522305 is a SNP in the phenylalanine hydroxylase (PAH) gene. A study of Caucasian cohorts, Bulgarian families, and African American families concluded that the more common rs1522305(G) allele was associated in the first two populations with increased risk for schizophrenia.
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Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia.
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schizophrenia the SNPs (rs1049623, rs2267641 and rs2239518) haplotype remaining significant even after adjustment for multiple testing (adjusted P=0.0136).
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[GWAS:Schizophrenia]
Frequency: 31.0%
References:3
References:3
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[GWAS:Schizophrenia]
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[GWAS:Schizophrenia]
Frequency: 33.6%
References:3
References:3
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blog Association of Circadian Genes with Mood Disorders *rs2287161 *rs10462028 *rs11123857 *rs17083008 *rs885861
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rs2234693 is a SNP upstream of the estrogen alpha receptor ESR1 gene, and is sometimes referred to as the -397T>C variation. rs2234693 rs9340799 and rs1256049 variations in ESR1 gene, in addition to the age of a woman, may predict the COH outcome in in vitro fertilization A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs2234693) and risk of ischemic stroke rs2234693(C;C)more frequent in African American schizophrenics (p=0.01 to 0.001). haplotype less common in schizophrenia rs2273206(T), rs2273207(G), rs2228480(G). Oestrogen receptor alpha gene haplotype and postmenopausal breast cancer risk: a case control study. Differential genetic effects of ESR1 gene polymorphisms on osteoporosis outcomes. Estrogen receptor alpha gene varia...
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rs2305767 (P = 1.16 x 10(-4); OR 1.41, 95% CI 1.18-1.67). We demonstrate significant association of allelic variants in MYO9B with schizophrenia Crohn's disease rs2305767 associated with inflammatory bowel disease (IBD) overall (corrected P-value 0.002, odds ratio [OR] 0.76, 95% confidence interval [CI] 0.67-0.86)
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schizophrenia *375 case and 812 control subjects *rs10399805 p = .018 and rs2275351; p = .008. [PharmGKB:Curated In a sample of 375 case and 812 control subjects a significant association of schizophrenia with this SNP (rs2275351) at intron 7 of CHI3L1 was identified.]
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Based on a study of 790 individuals from 245 nuclear families (220 families were European Caucasian; 300 of the probands had a diagosis of schizophrenia), the rs2070106(G) allele was overtransmitted to affected offspring. This actually conflicts with a previous report in which the rs2070106(A) allele was identified (also in Caucasians) in a combined gene association/expression study as associated with schizophrenia. This is either a case of the 'flip-flop' phenomenon in which multilocus effects and variation in interlocus correlations reverse a previously reported association, or perhaps more likely, a false positive.
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rs7527939 is a C/T polymorphism located in the second intronic region of the hedgehog acyltransferase gene (HHAT), located on human chromosome 1 1 . HHAT, also known as SKI1, is responsible for an enzyme that catalyzes amino-terminal palmitoylation 2 of hedgehog (SHH) through the secretory pathway 3, . According to dbSNP, the ancestral allele is C, and the minor allele frequency from the 1000 Genomes Project is 26.6% 1. Population-specific allele frequencies from the International HapMap Project are given below in graphic form. A GWAS found a significant association between rs7527939 and a diagnosis of schizophrenia or schizoaffective disorder in a Bulgarian population. Using 188 affected and 376 unaffected individuals, the study tested 554, 496 SNPs for association with schizophrenia. Aft...
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rs7624540, rs4072520, rs6779828 showed genotypic association with schizophrenia
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rs795009 and rs310762 have been linked to schizophrenia
Frequency: 38.9%
References:2
References:2
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One of the only SNPs in a large GWAS study to have statistical significance in terms of helping to predict anti-psychotic drug (ziprasidone in this case) response by schizophrenia patients. [GWAS:Treatment response to antipsychotics]
Associated with ADHD
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SNPs nominally associated with schizophrenia (rs3787283, rs3746544) were the same as those previously demonstrated to be associated with ADHD but with the opposite alleles, allowing the intriguing hypothesis that genetic variation at SNAP25 may be differentially associated with both schizophrenia and ADHD When comparing pooled results of multiple ADHD studies, only rs3746544(A) was found to have a significant association (p=0.028) with slightly increased risk (OR 1.15 at 95%) of ADHD. Support for the MnlI polymorphism of SNAP25; a Korean ADHD case-control study. Investigation of variation in SNAP-25 and ADHD and relationship to co-morbid major depressive disorder. Biased paternal transmission of SNAP-25 risk alleles in attention-deficit hyperactivity disorder.
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rs7624540, rs4072520, rs6779828 showed genotypic association with schizophrenia
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[PharmGKB:Non-Curated GWAS Results: Identification of loci associated with schizophrenia by genome-wide association and follow-up (Initial Sample Size: 479 cases, 2,937 controls; Replication Sample Size: 6,666 cases, 9,897 controls; Risk Allele: rs7192086-T). This variant is associated with Schizophrenia.] [OMIM:BSCL2 GENE; BSCL2] [GWAS:Schizophrenia]
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rs762178 seems to be a potential candidate in altering risk for schizophrenia in the Chinese Han population. [OMIM:OLIGODENDROCYTE LINEAGE TRANSCRIPTION FACTOR 2; OLIG2]
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[PharmGKB:Non-Curated GWAS results: A Genome-Wide Association Study of Schizophrenia Using Brain Activation as a Quantitative Phenotype. (Initial Sample Size: 64 cases, 74 cases; Replication Sample Size: NR); (Region: 3p12.3; Reported Gene(s): ROBO2, ROBO1; Risk Allele: rs9836484-?); (p-value= 0.000004).This variant is associated with Brain imaging in schizophrenia (interaction).] [GWAS:Brain imaging in schizophrenia (interaction)]
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associated with schizophrenia rs10790212-rs4938445-rs497768 [OMIM:FXYD DOMAIN-CONTAINING ION TRANSPORT REGULATOR 6; FXYD6]
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[PharmGKB:Non-Curated GWAS results: A Genome-Wide Association Study of Schizophrenia Using Brain Activation as a Quantitative Phenotype. (Initial Sample Size: 64 cases, 74 cases; Replication Sample Size: NR); (Region: 5q23.2; Reported Gene(s): CTXN3, SLC12A2; Risk Allele: rs245201-?); (p-value= 0.00000009).This variant is associated with Brain imaging in schizophrenia (interaction).] [GWAS:Brain imaging in schizophrenia (interaction)]
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schizophrenia rs1049623 associated with schizophrenia (odds ratio=1.44, 95% confidence interval: 1.15-1.79, adjusted P=0.0016). schizophrenia the SNPs (rs1049623, rs2267641 and rs2239518) haplotype remaining significant even after adjustment for multiple testing (adjusted P=0.0136). [PharmGKB:Curated Risk or phenotype-associated allele, tested allele: unspecified; minor allele designation varies by ethnicity in dbSNP Phenotype: In 114 cases and 414 controls (n = 528), univariate analysis of disease association showed OR = 0.69 for heterozygote, OR = 1.04 for homozygous, versus homozygous wild type, in ALL, with P(trend) OR = 0.96, p = 0.78 using an additive model. Study size: 528. Study population/ethnicity: Childhood acute lymphoblastic leukemia (<=14 years) and healthy newborn contro...
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[GWAS:Schizophrenia]
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part of a three marker haplotype rs737865-rs4680-rs165599 COMT haplotypes at rs737865 and rs165599 may predict a favorable outcome for bupropion treatment for smoking cessation. We have typed the IVS 1 rs737865 and 3' rs615599 sites and also included a novel IVS 1 indel polymorphism. We report that the schizophrenia-associated haplotype is significantly heterogeneous in populations worldwide. may affect non-Hodgkin lymphoma, anxiety-related personality traits Also mentioned in these PMIDs * * * * * * [PharmGKB:Curated This variant may predict a favorable outcome for bupropion treatment for smoking cessation] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
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[GWAS:Schizophrenia]
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Located within intron 8 of the neurotransmitter type A gamma-aminobutyric acid (GABA) A receptor, beta 2 gene, more often as well as officially called GABRB2. This SNP, or more precisely certain haplotypes associated with it, has been linked to schizophrenia, and in particular systematic schizophrenia, in studies on Japanese, Chinese, and German populations . A fascinating and complex argument has been made suggesting that changes in our environment have led to positive selection for the rs1816071(G) containing haplotypes also now seen at increased frequency in schizophrenics . popular in pubmed
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[PharmGKB:Non-Curated GWAS results: Genomewide association for schizophrenia in the CATIE study: results of stage 1 (Initial Sample Size: 738 cases, 733 controls; Replication Sample Size: NR). This variant is associated with Schizophrenia.] [GWAS:Schizophrenia]
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g2b2mh (sourced from ) rs3800779 rs748693 and rs1036145 are associated with a variety of brain parameters such as hippocampal volume, hippocampal activity (declarative memory task) and activity in the dorsolateral prefrontal cortex (DLPFC). The main suggestion of how these variants in KCNH2 might lead to these brain changes and risk for schizophrenia comes from previous findings that mutations in this gene screw up the efflux of K+ ions during the repolarization phase of an action potential.
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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SNPs nominally associated with schizophrenia (rs3787283, rs3746544) were the same as those previously demonstrated to be associated with ADHD but with the opposite alleles, allowing the intriguing hypothesis that genetic variation at SNAP25 may be differentially associated with both schizophrenia and ADHD
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implicated in schizophrenia
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Genetic variation in the serotonin 2A receptor and suicidal ideation in a sample of 270 Irish high-density schizophrenia families.
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rs1046089 is a SNP in the HLA-B associated transcript 2 BAT2 gene. A study of 2,162 case-controls found an association between rs1046089 and severe malaria. [GWAS:None]
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schizophrenia rs7715300 (p = 0.001) and rs6897690 (p = 0.032)
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This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs7582658, was deemed to be the core SNP of a region on chromosome 2 with 274 SNPs spanning 2282KB from 2:188489676 to 2:190772106 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation as...
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linked to schizophrenia with rs7598440, rs839523, and rs707284 [OMIM:V-ERB-B2 AVIAN ERYTHROBLASTIC LEUKEMIA VIRAL ONCOGENE HOMOLOG 4; ERBB4]
Frequency: 49.6%
References:1
References:1
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[GWAS:Schizophrenia]
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This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs2437896, was deemed to be the core SNP of a region on chromosome 2 with 115 SNPs spanning 774KB from 2:175671012 to 2:176445047 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation as ...
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Common variants in the ATM, BRCA1, BRCA2, CHEK2 and TP53 cancer susceptibility genes are unlikely to increase breast cancer risk. LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs.
Normal risk of developing schizophrenia
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This snp is in the Pseudoautosomal region. rs6603272, part of a haplotype block spanning introns 4, 5 and 6 of the IL3RA gene, has been reported in a whole genome association study to be associated with schizophrenia. (The other SNPs in this block are rs6422441 and rs17883192.) The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with this allele is 2.74.
Frequency: 53.6%
References:1
References:1
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[GWAS:Schizophrenia]
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[GWAS:Schizophrenia]
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[GWAS:Schizophrenia]
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Common variants at VRK2 and TCF4 conferring risk of schizophrenia. [GWAS:Schizophrenia]
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[GWAS:Schizophrenia]
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Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia.
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showed that rs947267 was significantly associated with schizophrenia rs778294 and rs947267 associated with the risk of schizophrenia, however rs947267, showed an opposite direction of genetic effect on schizophrenia risk here than in a previous study
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Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia. Usefulness of direct sequencing of pooled DNA for SNP identification and allele-frequency determination compatible with a common disease/common variant hypothesis. Publicly Available Single Nucleotide Polymorphisms in Genes Possibly Susceptible to Antiepileptic Drug Resistance in Healthy Koreans Development of a high-throughput microarray-based resequencing system for neurological disorders and its application to molecular genetics of amyotrophic lateral sclerosis.
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rs1176713 is a SNP, also known as g.14396A>G, in the 5-hydroxytryptamine (serotonin) receptor 3A HTR3A gene. rs1176713 may be a useful predictor of therapeutic response to risperidone treatment in Chinese schizophrenia patients
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rs211105, rs1800532 and rs7933505 related to schizophrenia Polymorphism screening and haplotype analysis of the tryptophan hydroxylase gene (TPH1) and association with bipolar affective disorder in Taiwan. Tryptophan hydroxylase gene 1 (TPH1) variants associated with cerebrospinal fluid 5-hydroxyindole acetic acid and homovanillic acid concentrations in healthy volunteers.
1.4x higher schizophrenia risk
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rs6277 (957C>T, Pro319Pro) is one of several SNPs in the dopamine receptor DRD2 gene. In a study of 300+ Russian patients with schizophrenia, the rs6277(C) allele was associated with higher risk. From a pooled meta-study (total of 4 other reports plus this one) the allelic odds ratio is 1.42 (CI: 1.26-1.61, p<0.00005), and the genotypic odds ratio for the (C;C) genotype was 1.6 (CI: 1.32-1.95, p<0.00005). Note that rs6275 and rs6277 are only 18bp apart, hence their very tight linkage (r<sup>2</sup>=1). gs278 reflects a gene-gene interaction between this SNP and a NR3A SNP, rs10989591, in which older adults with a particular combination of genotypes at these two (independent) loci are reported to exhibit better episodic memory. C allele associated significantly (p = 0.0...
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Rs1062613 (C178T, Pro16Ser) is located within the 5' UTR of HTR3A and may effect HTR3A expression. reporter constructs containing the T allele showed increased HTR3A expression compared to the C allele CC and CT carriers associated with higher harm avoidance (p = 0.04) scores in 2 sample groups of Swedish women (366 in total), and non-conformity in 1 sample no significant association between treatment-resistant schizophrenia and Rs1062613, however, maintenance neuroleptic dose was significantly higher for TT carriers (p = 0.041) [PharmGKB:Curated This promoter variant regulates expression of the gene. The T allele is associated with increased expression.]
Frequency: 61.5%
References:1
References:1
Frequency: 61.9%
References:4
References:4
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Category:is a snp associated with schizophrenia rs10790212-rs4938445-rs497768 [OMIM:FXYD DOMAIN-CONTAINING ION TRANSPORT REGULATOR 6; FXYD6]
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[GWAS:Schizophrenia]
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This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs2499846, was deemed to be the core SNP of a region on chromosome 1 with 173 SNPs spanning 574KB from 1:158440777 to 1:159015569 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation as ...
1.1x increased risk for schizophrenia
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rs6932590 is a SNP that is postulated to have a role in conferring increased susceptibility for schizophrenia. rs6932590 lies in the major histocompatibility complex (MHC) region on chromosome 6, a region that codes for several genes with significant roles in autoimmunity, such as human leukocyte antigens. Specifically, rs6932590 lies in an intergenic region between PRSS16 (a serine protease expressed in the thymus that plays a role in positive T cell selection) and POM121L2 (a membrane glycoprotein) . The T allele at rs6932590 purportedly confers an increased risk for schizophrenia, with reported odds ratios of 1.16 and 1.31 . === Evidence === One large-scale case-controlled genome-wide association study (GWAS) that examined differential genotypes in individuals with schizophrenia, found ...
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[GWAS:Schizophrenia]
Frequency: 66.4%
References:1
References:1
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[GWAS:Schizophrenia]
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[GWAS:Schizophrenia]
Frequency: 69.0%
References:11
References:11
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23andMe blog schizophrenia *rs3131296(C) increased the odds of schizophrenia by 1.19x *rs12807809(T) increased the odds of schizophrenia by 1.15x *rs9960767(C) increased the odds of schizophrenia by 1.23 times. Although several of the SNPs reported in to be associated with increased risk for schizophrenia were replicated in this study of Han Chinese, rs12807809 did not (i.e. it was not found to be associated with increased risk in this study of ~2,500 Chinese patients). New Genetic Findings in Schizophrenia: Is there Still Room for the Dopamine Hypothesis of Schizophrenia? A neuropsychological investigation of the genome wide associated schizophrenia risk variant NRGN rs12807809. Genetic and functional analysis of the gene encoding neurogranin in schizophrenia. [OMIM:?] [GWAS:Schizophreni...
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[GWAS:Schizophrenia]
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[GWAS:Schizophrenia]
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[GWAS:Schizophrenia]
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schizophrenia p = 0.035
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Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia.
normal risk of schizophrenia in limited study
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Associated with schizophrenia in a study of Croatians. Due to the limited number and diversity of the studied population, more study is needed to confirm any link. The T allele was associated with a decreased risk of schizophrenia.
Frequency: 77.9%
References:1
References:1
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[GWAS:Schizophrenia]
Frequency: 78.8%
References:1
References:1
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rs6584400 is a SNP in the neuregulin 3 NRG3 gene. Based on a study of 1515 Ashkenazi Jewish individuals, including 285 parent-child trios, 173 unrelated cases, and 487 unrelated controls, three SNPs (rs10883866, rs10748842, and rs6584400) were found to be associated with the 'delusion' factor as a quantitative trait in schizophrenia, even though no SNP in this study withstood multiple test correction for association with the binary schizophrenia phenotype itself. After replication in an independent set of 153 Ashkenazi Jewish samples, the empirical study-wide significance across all 9 factors studied was estimated to be p = 2.7x10e-3. [PharmGKB:Curated In a study of Ashkenazi Jewish SZ (schizophrenia and schizoaffective disorder),the minor allele (A) of rs6584400 was found to be associate...
Frequency: 83.2%
References:1
References:1
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[GWAS:Schizophrenia]
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schizophrenia rs7715300 (p = 0.001) and rs6897690 (p = 0.032)
Frequency: 89.8%
References:1
References:1
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[GWAS:Schizophrenia]
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[GWAS:Schizophrenia]
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rs1006615 is associated with increased risk for schizophrenia in German and Scandinavian samples
References:1
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This snp has been linked to schizophrenia.
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anxiety-related personality traits, ADHD, schizophrenia part of a three marker haplotype rs737865-rs4680-rs165599 epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes popular in pubmed is associated with bipolar disorder and influences prefrontal aspects of verbal memory in bipolar patients and healthy controls. [PharmGKB:Curated In a study of 78 African American and 65 white patients diagnosed with schizophrenia or schizoaffective disorder, this SNP in the COMT gene was found to have significant associations with response to risperidone over 2-12 weeks in both African-American and white patients.] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
possible weight gain if taking olanzapine
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rs3813929, also known as -759C/T, is a SNP in the 5-hydroxytryptamine (serotonin) receptor 2C HTR2C gene. A study of 107 patients with schizophrenia being treated with olanzapine reported a protective effect against weight-gain from the (T) allele of this SNP; zero patients (of 28) with a rs3813929(T) allele had a body mass index increase of >=10% (p=0.002), whereas (C;C) homozygotes did. This effect may also involve nearby SNP rs518147. T allele showed borderline significant association with higher BMI and incidence of lifetime major depressive disorder among 4978 persons from the European Prospective Investigation into Cancer (EPIC)-Norfolk study, however, only the association with BMI remained borderline significant within the full EPIC-Norfolk cohort (20,981 persons) The association...
complex; possible association with anxiety related behaviours
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In mice, the genetic locus best correlated to anxiety-related behaviour contains the 'regulator of G protein signaling 2' gene . In humans, SNPs in the equivalent RGS2 gene have now been studied to see if they are correlated to anxiety related disorders. In the first part of one study, 119 families including children underwent standard lab-based behavioural assessments of behavioural inhibition, defined as a heritable temperamental profile characterized by a tendency to be shy, avoident, and behaviourally restrained in situations that are novel or unfamiliar. Along with some other RGS2 SNPs, carriers of a rs4606(G) allele were 3 fold more likely to exhibit behavioural inhibition (CI: 1.31-6.84, p = 0.0026). In the second part of this study, 744 college undergraduates (228 men, 516 women) w...
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Genetic variation in the serotonin 2A receptor and suicidal ideation in a sample of 270 Irish high-density schizophrenia families.
Carrier for rs6994992(T;T) which one report has associated with both creativity and schizophrenia
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also known as SNP8NRG243177 Initial reports of a link to schizophrenia remain inconclusive. paper implicated in schizophrenia effects white matter density and integrity schizophrenia risk-associated The neuregulin 1 promoter polymorphism rs6994992 is '''not''' associated with neurocognition or chronic schizophrenia in a study of 738 patients T allele (in a per allele fashion) significantly associated with lateral ventricle volume in 95 first-episode schizophrenics points out that their result is that (T) was weakly associated with schizophrenia, however this is the opposite of the original association study where the C allele. [OMIM:NEUREGULIN 1; NRG1]
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linked to schizophrenia with rs7598440, rs839523, and rs707284 Disease-associated intronic variants in the ErbB4 gene are related to altered ErbB4 splice-variant expression in the brain in schizophrenia. Neuregulin 1 in neural development, synaptic plasticity and schizophrenia. A genome-wide investigation of SNPs and CNVs in schizophrenia. Analysis of association between common SNPs in ErbB4 and bipolar affective disorder, major depressive disorder and schizophrenia in the Han Chinese population. The effects of psychosis risk variants on brain connectivity: a review. [OMIM:V-ERB-B2 AVIAN ERYTHROBLASTIC LEUKEMIA VIRAL ONCOGENE HOMOLOG 4; ERBB4]
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13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. *rs751229(T) and rs3738401(A) was over-transmitted to males with psychotic disorder. *under-transmitted rs821616(T) and rs1411771(T) *The risk haplotype for psychotic disorder also associated to perseverations (P = 0.035; for rs751229 alone P = 0.0012), and a protective haplotype G-T-G with rs1655285 in addition to auditory attention (P = 0.0059). [OMIM:SCHIZOPHRENIA, SUSCEPTIBILITY TO]
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. The association between several SNPs in the DTNBP1 gene, most especially rs760761, and schizophrenia was confirmed in a new sample of 1021 cases and 626 controls from Ireland. Genetic variation in the 6p22.3 gene DTNBP1, the human ortholog of the mouse dysbindin gene, is associated with schizophrenia. Support for association of schizophrenia with genetic variation in the 6p22.3 gene, dysbindin, in sib-pair families with linkage and i...
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G allele associated with schizophrenia among 120 (likely Japanese) first-episode neuroleptic-naive schizophrenics treated with risperidone genotyped for 30 variants in misc. dopamine and serotonin (receptors and otherwise) two SNPs in DRD2 (rs1799989 and rs1800497) and two SNPs in AKT1 (rs3803300 and rs2494732) were significant predictors of treatment response to risperidone The ancestral allele is G in the dbSNP database. [PharmGKB:Curated This SNP is significant predictor of treatment response to risperidone in first-episode schizophrenia.]
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associations with schizophrenia and herpes rs2272127 with schizophrenia(P = 0.0007, odds ratio for C allele 1.49, 95% CI: 1.18-1.87; P = 0.03 following correction for multiple comparisons). rs2272127 was also associated with herpes simplex virus 1 (HSV1) seropositivity in cases (P = 0.04, OR for G allele 1.58, 95% CI: 1.04-2.39).
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[GWAS:None]
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Category:is a snp associated with schizophrenia rs10790212-rs4938445-rs497768 No association between the FXYD6 gene and schizophrenia in the Chinese Han population. Failure to confirm genetic association of the FXYD6 gene with schizophrenia: the Japanese population and meta-analysis. [OMIM:FXYD DOMAIN-CONTAINING ION TRANSPORT REGULATOR 6; FXYD6]
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This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs2848745, was deemed to be the core SNP of a region on chromosome 18 with 119 SNPs spanning 597KB from 18:37022928 to 18:37619977 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation as...
less weight gain if taking olanzapine
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rs518147, also known as -697G/C, is a SNP in the 5-hydroxytryptamine (serotonin) receptor 2C HTR2C gene. A study of 107 patients with schizophrenia being treated with olanzapine reported a protective effect against weight-gain from the (C) allele of this SNP; fewer patients (of 28) with a rs518147(C) allele had a body mass index increase of >=10% (p=0.0006), whereas (G;G) homozygotes did. This effect may also involve nearby SNP rs3813929. The association between HTR2C polymorphisms and obesity in psychiatric patients using antipsychotics: a cross-sectional study. The association between HTR2C gene polymorphisms and the metabolic syndrome in patients with schizophrenia. Multivariate permutation analysis associates multiple polymorphisms with subphenotypes of major depression. HTR2C gene ...
common
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Located in the Pseudoautosomal region rs4129148, located near the CSF2RA gene, has been reported in a whole genome association study to be associated with schizophrenia. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with this allele is 3.23 (CI 2.04 - 5.15). Given the results from the recent massive Psychiatric Genomics Consortium GWAS, it appears very unlikely that any large effect common SNPs exist for schizophrenia. It is not completely clear, though, how the previously replicated results for rs4129148 might be explained. It is currently predicted that 10,000 SNPs contribute to schizophrenic illness. The diagnosis for schizophrenia has now possibly shifted from asking: Schizophrenic? Yes or No to How much Schizophrenic? [GWAS:Schizophrenia]
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rs10883866 is a SNP in the neuregulin 3 NRG3 gene. Based on a study of 1515 Ashkenazi Jewish individuals, including 285 parent-child trios, 173 unrelated cases, and 487 unrelated controls, three SNPs (rs10883866, rs10748842, and rs6584400) were found to be associated with the 'delusion' factor as a quantitative trait in schizophrenia, even though no SNP in this study withstood multiple test correction for association with the binary schizophrenia phenotype itself. After replication in an independent set of 153 Ashkenazi Jewish samples, the empirical study-wide significance across all 9 factors studied was estimated to be p = 2.7x10e-3. [PharmGKB:Curated In a study of Ashkenazi Jewish SZ (schizophrenia and schizoaffective disorder),the minor allele (G) of rs10883866 was found to be associa...
common
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rs17883192, part of a haplotype block spanning introns 4, 5 and 6 of the IL3RA gene, has been reported in a whole genome association study to be associated with schizophrenia. (The other SNPs in this block are rs6422441 and rs6603272.) The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with this allele is 3.07.
normal cognitive ability
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
normal
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rs1800169 is a SNP in the ciliary neurotrophic factor CNTF gene. In a study of 417 patients with schizophrenia, 279 were treated with iloperidone while 138 were treated with placebo. Iloperidone significantly improved in 6 clinical scores versus placebo. rs1800169(G;G) homozygotes showed greater improvement with iloperidone compared to placebo for 3 of the clinical scores compared to carriers of a rs1800169(A) allele. [PharmGKB:Curated Schizophrenia patients with homozygous G/G for the rs1800169 show better response to iloperidone.]
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This snp in the gene ZDHHC8 does not appear to have any link to schizophrenia despite being quite popular in pubmed [OMIM:ZINC FINGER DHHC DOMAIN-CONTAINING PROTEIN 8; ZDHHC8]
common in clinvar
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rs3738401 is a SNP in the DISC1 gene, known as R264Q. Associated with schizophrenia 13 single-nucleotide polymorphisms (SNPs) in 723 members of 179 Finnish Bipolar disorder families. *rs751229(T) and rs3738401(A) was over-transmitted to males with psychotic disorder. *under-transmitted rs821616(T) and rs1411771(T) *The risk haplotype for psychotic disorder also associated to perseverations (P = 0.035; for rs751229 alone P = 0.0012), and a protective haplotype G-T-G with rs1655285 in addition to auditory attention (P = 0.0059). [OMIM:DISRUPTED IN SCHIZOPHRENIA 1; DISC1]
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rs1801131 is a SNP in the MTHFR gene, representing an A>C mutation at mRNA position 1298, resulting in a glu429-to-ala (E429A) substitution (hence this SNP is also known as A1298C or E429A). A diplotype (according to the authors, but perhaps actually a genoset) of rs1801131 and rs1801133 has been linked to increased risk for several types of brain cancer. The highest risk of meningioma was associated with heterozygosity for both MTHFR SNPs (odds ratio 2.11, CI: 1.42-3.12, p=0.002). The corresponding odds ratio for glioma was 1.23 (CI: 0.91-1.66, p=0.02. In general, risks were increased with genotypes associated with reduced MTHFR activity. rs1801131 shows no consistent association with schizophrenia overall in 12 studies totaling 3,000+ patients [PharmGKB:Curated Risk or phenotype-asso...
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23andMe blog rs1006737 or (rs2159100) Each T at this SNP increased the odds of bipolar disorder by 1.18 times compared to having two CC copies [PharmGKB:Curated A genome-wide association analysis study in 4,387 cases and 6,209 controls identified a strong association of this variant in the CACNA1C gene with bipolar disorder.] [OMIM:MAJOR AFFECTIVE DISORDER 9; MAFD9] [GWAS:Bipolar disorder]
normal
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rs6280, also known as '''Ser9Gly''', is a SNP in the dopamine receptor D3 DRD3 gene. The rs6280(C) allele encodes a glycine, and the (T) allele encodes a serine (in dbSNP orientation). In a study of 88 patients being treated for schizophrenia with olanzapine, those who were rs6280(C;C) homozygotes had greater positive symptom remission (endpoint rating of minimal or none on all PANSS clinical response positive items, 39.1%), as compared with (C;T) or (T;T) genotypes (13.8%; p = 0.033). Ser9Gly has been implicated in executive function in some studies, but the results are conflicting. * Gly/Gly carriers showed significantly (p = 0.002) poorer performance than Ser/Ser carriers on executive functioning tasks in a somewhat small Caucasian sample (84 patients with first-episode psychosis and 85...
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
Magnitude: 0
Frequency: 51.8%
References:5
Frequency: 51.8%
References:5
normal
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rs11868035 is one of several SNPs associated with the SREBF1 gene that show a modest association with type-2 diabetes. A study of ~2,000 Caucasian patients (and 10,000+ controls) led to an odds ratio of 1.19 (CI: 1.07-1.33, p=0.002) for the minor (risk) allele, rs11868035(A), in the orientation as in dbSNP. type-2 diabetes rs2297508(C) and rs11868035(C) This SNP rs11868035 and rs1057217 are associated with increased risk of schizophrenia in German and Scandinavian samples. This SNP and rs6812193 are reported to affect risk of Parkinson's disease. plos Polymorphisms in the gene encoding sterol regulatory element-binding factor-1c are associated with type 2 diabetes. [PharmGKB:Curated This SNP in the SREBF1 gene was strongly associated with schizophrenia in German, Danish and Norwegian samp...
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plos () - The minor alleles of rs4819756 and rs2870983 were significantly negatively associated with schizophrenia
Magnitude: 0
Frequency: 61.1%
Repute:Good
References:3
Frequency: 61.1%
Repute:Good
References:3
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Genomewide association for schizophrenia in the CATIE study: results of stage 1 (Initial Sample Size: 738 cases, 733 controls; Replication Sample Size: NR). This variant is associated with Schizophrenia.] [GWAS:Schizophrenia]
normal
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rs4320932 is a SNP in the IF2 insulin-like growth factor 2 gene. A study totaling ~5,000 non-Hispanic white patients with ovarian cancer found a 13% decreased risk of ovarian cancer per copy of the rs4320932(G) allele carried (CI: 0.81-0.93, P-trend=7.4 × 10e-5). Associated with schizophrenia in a study of Croatians. Due to the limited number (~100 patients) and diversity of the studied population, more study is needed to confirm any link. The G allele was associated with an increased risk of schizophrenia with P < 0.001. Small size study with 212 cases linked the G allele earlier found protective against ovarian cancer increasing relapse by 3.05 (95% confidence interval CI: 1.47–6.37, P-trend 2*10e-4) and mortality 3.28 (95% CI: 1.64–6.57, P-trend 6*10e-5). Association...
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
Magnitude: 0
Frequency: 74.3%
Repute:Good
References:2
Frequency: 74.3%
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: A Genome-Wide Association Study of Schizophrenia Using Brain Activation as a Quantitative Phenotype. (Initial Sample Size: 64 cases, 74 cases; Replication Sample Size: NR); (Region: 14q32.32; Reported Gene(s): TRAF3; Risk Allele: rs10133111-?); (p-value= 0.000005).This variant is associated with Brain imaging in schizophrenia (interaction).] [GWAS:Brain imaging in schizophrenia (interaction)]
Magnitude: 0
Frequency: 80.5%
Repute:Good
References:3
Frequency: 80.5%
Repute:Good
References:3
common on affy axiom data
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[PharmGKB:Non-Curated GWAS Results: A genome-wide association study in 574 schizophrenia trios using DNA pooling (Initial Sample Size: 574 cases, 605 controls, 1,148 parents of cases; Replication Sample Size: NR; Risk Allele: rs11064768-A).] [GWAS:Schizophrenia]
common on affy axiom data
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Persistence criteria for susceptibility genes for schizophrenia: a discussion from an evolutionary viewpoint. [PharmGKB:Non-Curated GWAS Results: Identification of loci associated with schizophrenia by genome-wide association and follow-up (Initial Sample Size: 479 cases, 2,937 controls; Replication Sample Size: 6,666 cases, 9,897 controls; Risk Allele: rs1602565-C). This variant is associated with Schizophrenia.] [GWAS:Schizophrenia]
common in complete genomics
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Genetic variation in the serotonin 2A receptor and suicidal ideation in a sample of 270 Irish high-density schizophrenia families.
normal
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23andMe blog schizophrenia *rs3131296(C) increased the odds of schizophrenia by 1.19x *rs12807809(T) increased the odds of schizophrenia by 1.15x *rs9960767(C) increased the odds of schizophrenia by 1.23 times. [OMIM:?] [GWAS:Schizophrenia]
higher risk for RA
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rs6314, also known as C1354T or His452Tyr/H452Y, is a SNP in the serotonin 2A receptor HTR2A gene. Based on a study of 166 Caucasian patients being treated for depression with paroxetine, rs6314 heterozygotes were associated with better response. There was a significantly higher frequency of heterozygotes in the remitter and response groups in comparison to the non-remitter (odds ratio 7.50, p=0.002) and non-response groups (odds ratio 5.25, p=0.01). * rs6314 is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6314(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs13286...
Magnitude: 0
Frequency: 91.0%
Repute:Good
References:2
Frequency: 91.0%
Repute:Good
References:2
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Genomewide association for schizophrenia in the CATIE study: results of stage 1 (Initial Sample Size: 738 cases, 733 controls; Replication Sample Size: NR). This variant is associated with Schizophrenia.] [GWAS:Schizophrenia]
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: A Genome-Wide Association Study of Schizophrenia Using Brain Activation as a Quantitative Phenotype. (Initial Sample Size: 64 cases, 74 cases; Replication Sample Size: NR); (Region: 6q16.2; Reported Gene(s): POU3F2; Risk Allele: rs9491640-?); (p-value= 0.000009).This variant is associated with Brain imaging in schizophrenia (interaction).] [GWAS:Brain imaging in schizophrenia (interaction)]
Magnitude: 0
Frequency: 94.7%
Repute:Good
References:1
Frequency: 94.7%
Repute:Good
References:1
Magnitude: 0
Frequency: 97.3%
Repute:Good
References:3
Frequency: 97.3%
Repute:Good
References:3
common in complete genomics
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A very large (ultimately over 7,000 cases spanning multiple European Caucasians) study concluded that rs17101921 showed evidence for association with schizophrenia, with an odds ratio of 1.17 (CI: 1.06-1.29, p=0.0009).
common
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[PharmGKB:Curated This study showed a highly significant association between a COMT haplotype of two functional SNPs (Ala72Ser and Val158Met) and aggressive behavior in schizophrenia.] [OMIM:SCHIZOPHRENIA, SUSCEPTIBILITY TO]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Genomewide association for schizophrenia in the CATIE study: results of stage 1 (Initial Sample Size: 738 cases, 733 controls; Replication Sample Size: NR). This variant is associated with Schizophrenia.] [GWAS:Schizophrenia]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Genomewide association for schizophrenia in the CATIE study: results of stage 1 (Initial Sample Size: 738 cases, 733 controls; Replication Sample Size: NR). This variant is associated with Schizophrenia.] [GWAS:Schizophrenia]
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located in 5' UTR of GRIN1 significant (p = .0000013) assoc. w/ schizophrenia in a sample of 2455 Han Chinese mentioned w/ possible schizophrenia association in a sample of 677 Germans (354 patients, 323 controls), but the initial association did not survive multiple correction [OMIM:GLUTAMATE RECEPTOR, IONOTROPIC, N-METHYL-D-ASPARTATE, SUBUNIT 1; GRIN1]
normal risk
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rs1801028 is a SNP in the dopamine D2 receptor DRD2 gene. A meta-analysis comprising 27 samples and over 3,707 schizophrenia patients concluded that Cys/Ser heterozygotes, i.e. rs1801028(C;G) genotypes, were at elevated risk for schizophrenia when compared to either homozygote genotype (rs1801028(C;C) or rs1801028(G;G)). The odds ratio was 1.4 (p<0.005). An earlier meta-analysis comprising over 9,000 schizophrenia patients concluded pretty much the same thing: the Cys311 (rs1801028(G)) allele frequency led to an odds ratio of 1.43 (CI: 1.16-1.78, p<0.001) for this risk allele. A study of ~120 Chinese patients with schizophrenia concluded that Cys/Ser heterozygotes may not respond to risperidone treatment as well as Ser/Ser homozygotes. A paper has been published describing mistakes m...
156 snps
(hide) Sciatica
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
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rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele in these positions increased the risk of disease (p=0.006 and, p=0.008, respectively). Carrying a haplotype with the G allele in all three promoter SNPs increased the risk of symptomatic DIP OA more than four-fold (OR 4.45, p=0.001). Carriage of the G-G diplotype indicated an increased risk of both symmetrical DIP OA (OR 1.52 95% CI 1.0...
common in complete genomics appears to be common on the 23andMe platform
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rs1800796 IL-6 572G>C polymorphism (and h.211 haplotype) is associated with abdominal aortic aneurysm (AAA). The risk allele is C. Our results provide evidence that there is a clear genetic influence of IL6 -572C>G polymorphism on plasma levels of fibrinogen and CRP, but this polymorphism does not lead to elevated blood pressure. rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele ...
3 snps
(hide) Scoliosis
Frequency: 15.9%
References:4
References:4
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The T allele of this SNP is associated with an increased risk of scoliosis in adolescent Japanese girls. [http://www.nature.com/ng/journal/v43/n12/full/ng.974.html] [GWAS:None]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 6q24.1; Reported Gene(s): GPR126); (p-value= 0.00000000004).This variant is associated with Height.] [OMIM:STATURE AS A QUANTITATIVE TRAIT] [GWAS:Height]
Frequency: 73.5%
References:0
References:0
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rs10738445 is a SNP in an intron of the BNC2 gene on chromosome 9. A GWAS study in Japanese and Han Chinese scoliosis patients found a significant (though small; odds ratio 1.21, p = 2.46 × 10e−13) association between rs10738445(A) and the disorder, and several lines of experiment evidence supported the hypothesis that increased BNC2 expression predisposes individuals to adolescent scoliosis (AIS).
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CHD7 gene polymorphisms are associated with susceptibility to idiopathic scoliosis. [OMIM:CHROMODOMAIN HELICASE DNA-BINDING PROTEIN 7; CHD7]
4 snps
(hide) Secondhand smoke susceptibility
normal asthma risk in certain populations
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common...
1 snp
(hide) Sickle Cell Anemia
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients
Frequency: 43.5%
References:0
References:0
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients
1.7x risk for priapism in SCA patients
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rs211239 is one of 2 SNPs (the other is rs2249358) in the KLOTHO gene found in a study of ~150 sickle cell anemia (SCA) patients to be associated with risk for priapism. The odds ratio is 1.7 (CI: 1.2-2.6) for carriers of a rs211239(C) allele, as in dbSNP orientation. [OMIM:KLOTHO; KL]
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients
lower risk
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rs736893 is related to sickle cell anemia, a genetic disease in which red blood cells form an abnormal crescent shape as opposed to the normal disc shape In the United States, it's estimated that sickle cell anemia affects 70,000–100,000 people, mainly African Americans. A New England Journal of Medicine study conducted in the US reported an average life expectancy of 42 in males and 48 in females . The landmark 1949 Science paper titled '[http://en.wikipedia.org/wiki/Sickle_Cell_Anemia,_a_Molecular_Disease Sickle Cell Anemia, a Molecular Disease by Pauling established the molecular basis for this sickle cell anemia and introduced notions that will become central to molecular medicine. Sickle cell leg ulcers are common complications of sickle cell anemia . As of 2010, despite the fac...
normal risk for priapism in SCA patients
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rs2249358 is one of 2 SNPs (the other is rs211239) in the KLOTHO gene found in a study of ~150 sickle cell anemia (SCA) patients to be associated with risk for priapism. The odds ratio is 2.6 (CI: 1.4-5.5) for carriers of a rs2249358(G) allele, as in dbSNP orientation. [OMIM:KLOTHO; KL]
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients Sickle Cell Disease in the Post Genomic Era: A Monogenic Disease with a Polygenic Phenotype.
10 snps
(hide) Sjogren-Larsson syndrome
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs72547571, also known as P315S or Pro315Ser, is a mutation in the fatty aldehyde dehydrogenase ALDH3A2 gene. Inherited as an autosomal recessive, two copies of the risk allele rs72547571(T), or one copy plus another defective ALDH3A2 allele, leads to Sjogren-Larsson syndrome. [OMIM:?]
1 snp
(hide) Sjögren's syndrome
Magnitude: 2
Frequency: 21.2%
Repute:Bad
References:29
Frequency: 21.2%
Repute:Bad
References:29
2x increased risk of developing SLE; 1.6x increased risk of developing primary biliary cirrhosis; and 1.7x increased risk of developing Sjögren's syndrome
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rs10488631, a SNP located 3' of the IRF5 gene, has been reported as a possibly causative SNP for systemic lupus erthymatosus (SLE), based on a study of ~700 Swedish patients. The risk allele is rs10488631(C), with a reported odds ratio of 2.07 (CI: 1.63-2.62, p = 9x10e-10). The C allele is also associated with primary biliary cirrhosis, with each C increasing the odds about 1.6 times. Each C allele increases risk of Sjögren's syndrome by 1.7 times. SLE rs10488631 and rs7582694 [OMIM:INTERFERON REGULATORY FACTOR 5; IRF5] [GWAS:Systemic lupus erythematosus]
normal risk of rheumatoid arthritis, SLE, Sjögren's syndrome, type-1 diabetes, and primary biliary cirrhosis.
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune dise...
Frequency: 61.9%
References:10
References:10
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[GWAS:Sjögren's syndrome]
common in complete genomics
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An association was found between Systemic lupus erythematosus (SLE) and rs5029939 (meta-analysis p = 2.89 x 10(-12), odds ratio 2.29). [PharmGKB:Curated GWAS results: Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus (Initial Sample Size: 431 cases, 2,155 controls; Replication Sample Size: 740 trios). This variant is associated with Systemic lupus erythematosus.] [OMIM:SYSTEMIC LUPUS ERYTHEMATOSUS, SUSCEPTIBILITY TO, 13; SLEB13] [GWAS:Systemic lupus erythematosus] [GWAS:Systemic lupus erythematosus]
4 snps
(hide) Skin cancer
0.78x decreased Basal Cell Carcinoma risk.
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
2-4x higher risk of sun sensitivity if part of risk haplotype. Increased risk of sunburns and freckles instead of tanning.
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rs1015362 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
2-4x higher risk of sun sensitivity if part of risk haplotype
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
Normal risk of Basal Cell Carcinoma. Normal risk for this kind of skin cancer.
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
common in clinvar
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rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair color (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. blog about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0005 Melanoma [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
normal
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rs2279744, a variant in the promoter of the MDM2 gene and also known as '-410T-G', 'SNP309', and 'SNP309T>G', has been studied for several years to determine it's role in cancer origin and treatment. The interest primarily stems from the ability of the MDM2 protein to bind to and thereby enhance the degradation of the tumor suppressor protein known as p53. Studies on rs2279744 include: * rs2279744(G) carriers in individuals with cancer tend to develop such cancers on average 12 years earlier than those lacking this allele, and the frequency of rs2279744(G) was greatly increased in those who developed soft tissue sarcomas at a young age. * Individuals with one or more rs2279744(G) alleles who are also carriers of the TP53 rs1042522(C) (arg at aa72) SNP tend to develop cancers earlier tha...
7 snps
(hide) SLC22A4 POLYMORPHISM
normal
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rs1050152, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T). A nearby SNP (rs2631367) in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%. [PharmGKB:Non-Curated Higher gabapentin exposure and lower renal clearance/tubular secretion in individuals carrying this variant] [OMIM:?]
1 snp
(hide) Smell
more able to detect β-ionone (floral) fragrance
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rs6591536, also known as N183D or Asn183Asp, is a SNP in the olfactory receptor, family 5, subfamily A, member 1 OR5A1 gene. The rs6591536(A) allele encodes the asparagine (N). Individuals vary in their ability to smell various odors, largely due to variations in their olfactory receptors. Carriers of one or two rs6591536(G) alleles can detect a particular compound, β-ionone, at levels two orders of magnitude lower than rs6591536(A;A) individuals. In fact, this study reports that 96% of the observed phenotypic variation is determined by this single SNP, making it nearly a completely Mendelian trait. People with high or low β-ionone sensitivity are found in all populations, and based on this SNP, variability was seen even in Neanderthal populations. Since rs6591536 determines ^...
1 snp
(hide) Smoking
A1/A2: Bad at avoidance of errors. 0.5x lower OCD risk, 0.87x lower Tardive Diskinesia risk, higher ADHD risk. More Alcohol Dependence. Lower risk of Postoperative Nausea. Increased obesity. Bupropion is not effective. The DRD2 TaqIA A1/A2 version causes less dopamine receptors. Doesn't learn from mistakes well. Reduced response to errors and increased addictive behavior Men may have half the risk of Obsessive Compulsive Disorder but higher risk of ADHD. Women have lower Persistence. 0.87x reduced risk of Tardive Diskinesia when taking dopamine receptor antagonists. Slightly increased risk of alcoholism and smoking addiction. Slower recovery from traumatic brain injury. Lower risk of postoperative nausea within 6 hours of surgery. Bupropion (Wellbutrin, Budeprion, Prexaton, Elontril, Aple...
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain . Reduced response to errors and increased addictive behavior It has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessa...
1.8x increased risk of lung cancer; reduced response to alcohol, therefore possibly increased risk of alcohol abuse
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rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...
apparently more prone to alcoholism interacts with the medicine Finasteride
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This SNP in the GABRA2 gene has been linked to Alcoholism. The effect of this SNP, a synonymous change at amino acid residue 132, is unknown, but it does not change the GABRA2 protein sequence. Carriers of at least one rs279858(G) allele respond slower to the effects of alcohol and are thereby apparently more prone to alcoholism than carriers of two rs279858(A) alleles. Finasteride, an FDA approved drug for the treatment of benign prostatic hypertrophy and a modulator of GABRA2, was shown to have more of a blocking effect on rs279858(A) homozygotes. Note that nearby SNPs have been grouped into a haplotype that shows statistically stronger association with alcohol dependence, namely the haplotype consisting of the rs279871(A) + rs279845(T) + rs279836(A) alleles . 1050 nicotine-dependent cas...
Alcohol Flush: Normal, doesn't flush. Normal hangovers. Normal risk of Alcoholism. Normal risk of Esophageal Cancer. Disulfiram is effective for alcoholism. Two working copies of Aldehyde Dehydrogenase (ALDH2) mean you won't turn bright red when you drink alcohol, unlike most Asians. After your body turns alcohol into the dangerous acetaldehyde, this gene quickly turns the acetaldehyde into vinegar. It also stops the acetaldehyde in cigarettes from causing Esophageal Cancer. It reduces hangovers compared to Asians, but less hangovers and flushing obviously increases the risk of alcoholism. Alcoholism can be treated effectively with the drug Disulfiram (Antabuse) which would stop this gene from working and cause the Asian flush in non-Asians. PMC2659709 [http://www.ncbi.nlm.nih.gov/pmc/art...
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rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Disulfiram (...
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[OMIM:?] [GWAS:Smoking behavior]
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 17p13.2; Reported Gene(s): CAMKK1; Risk Allele: rs758642-?); (p-value= 0.000007).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 4q28.1; Reported Gene(s): Intergenic); (p-value= 0.000009).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 3q24; Reported Gene(s): Intergenic; Risk Allele: rs800082-?); (p-value= 0.000003).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 16p13.2; Reported Gene(s): Intergenic; Risk Allele: rs3112740-?); (p-value= 0.000006).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 14q24.1; Reported Gene(s): ACTN1; Risk Allele: rs2268983-?); (p-value= 0.000007).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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[OMIM:?] [GWAS:Smoking behavior]
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated A study on 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry found first evidence for the involvement of DDC in the susceptibility to nicotine dependence. This variant in the DDC gene is part of t...
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[GWAS:Smoking behavior]
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 1p22.3; Reported Gene(s): AK002179); (p-value= 0.000003).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated In a total of 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry, this SNP in the DDC gene was significantly associated with two of the three adjusted nicotine dependence measures in the European-A...
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 3q13.12; Reported Gene(s): BBX); (p-value= 0.0000002).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 1p35.2; Reported Gene(s): Intergenic); (p-value= 0.000003).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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part of a three marker haplotype rs737865-rs4680-rs165599 COMT haplotypes at rs737865 and rs165599 may predict a favorable outcome for bupropion treatment for smoking cessation. We have typed the IVS 1 rs737865 and 3' rs615599 sites and also included a novel IVS 1 indel polymorphism. We report that the schizophrenia-associated haplotype is significantly heterogeneous in populations worldwide. may affect non-Hodgkin lymphoma, anxiety-related personality traits Also mentioned in these PMIDs * * * * * * [PharmGKB:Curated This variant may predict a favorable outcome for bupropion treatment for smoking cessation] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 7p15.2; Reported Gene(s): Intergenic; Risk Allele: rs886716-?); (p-value= 0.000008).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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1050 nicotine-dependent cases and 879 non-dependent smoking controls rs279858 and rs16859834 aka rs2229940
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated A study on 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry found first evidence for the involvement of DDC in the susceptibility to nicotine dependence. This variant in the DDC gene is part of t...
Frequency: 52.2%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 9q31.1; Reported Gene(s): Intergenic); (p-value= 0.000006).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 9p21.2; Reported Gene(s): Intergenic); (p-value= 0.000006).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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635 lung cancer cases with onset of disease below 51 years of age and 1,300 controls. major alleles associated with increased in risk of early-onset lung cancer modified by smoking. *rs1938901 (P = 0.0089) *rs193008 (P = 0.0108) *rs996999 (P = 0.0459). For rs996999, significance vanished after correction for multiple testing. odds ratio between 1.2 and 1.3 (95% confidence interval, 1.0-1.5)
Frequency: 60.2%
References:5
References:5
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 18q11.2; Reported Gene(s): CABLES1); (p-value= 0.000006).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 3q27.2; Reported Gene(s): Intergenic; Risk Allele: rs6444087-?); (p-value= 0.000009).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
Frequency: 65.5%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 4q31.1; Reported Gene(s): SET7); (p-value= 0.000008).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 5q14.3; Reported Gene(s): LOC133789; Risk Allele: rs933688-?); (p-value= 0.000006).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
References:5
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smoking http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.572.html [OMIM:?]
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 13q33.1; Reported Gene(s): Intergenic); (p-value= 0.000008).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 12q21.33; Reported Gene(s): Intergenic; Risk Allele: rs1847461-?); (p-value= 0.000008).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
normal risk
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rs1799724, a SNP near the tumor necrosis factor TNF gene, was found in a study of ~500 Caucasians to be both an independent risk factor for the development of Alzheimer's disease and also a modifier of the risk for individuals carrying ApoE4 alleles. On its own, the rs1799724(T) allele led to an odds ratio of 1.63 (CI: 1.13-2.34, p=0.009). In carriers of ApoE4 alleles, the odds ratio changed from 2.92 (CI: 2.00-4.27) in the absence of rs1799724(T) to an OR of 6.65 (CI: 3.26-13.55, p=0.03) in its presence. In a Chinese study , post-menopausal women were significantly more likely to have low bone mineral density if they had *CC-AA genotypes in rs1799724-rs1800629 * a haplotype of rs1799724-rs1800629-rs6254-rs6256-IL-1ra-rs2227956-rs1801197 news cigarette smoking and gastric cancer risk [Pha...
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 12q21.2; Reported Gene(s): Intergenic); (p-value= 0.000005).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
Magnitude: 0
Frequency: 92.0%
Repute:Good
References:0
Frequency: 92.0%
Repute:Good
References:0
common in complete genomics
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rs17041183 is in linkage disequilibrium with a polymorphism that increases susceptibility to Substance dependence, Nicotine 2.09 times for carriers of the G allele
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: Xq23; Reported Gene(s): TRPC5; Risk Allele: rs7050529-?); (p-value= 0.000006).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
Magnitude: 0
Frequency: 94.7%
Repute:Good
References:2
Frequency: 94.7%
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Genome-wide and candidate gene association study of cigarette Smoking behaviors. (Initial Sample Size: 4,611 individuals (2,617 smokers); Replication Sample Size: NR); (Region: 19p12; Reported Gene(s): ZNF505; Risk Allele: rs10411195-?); (p-value= 0.000006).This variant is associated with Smoking behaviors.] [GWAS:Smoking behaviors]
Magnitude: 0
Repute:Good
References:75
Repute:Good
References:75
normal
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rs11200638, a SNP in the HTRA1 promoter, is associated with a 10 fold increased risk of wet age related macular degeneration in Japanese and Caucasian populations. Further confirmed . The genotype at highest risk is (A;A). Note, most studies have shown that that this SNP is highly predictive (i.e. is in near perfect (D'>0.98) linkage disequilibrium) with rs10490924, thus the status of one very closely predicts the status of the other. However, one Caucasian AMD study reported the linkage disequilibrium measure for these two SNPs on 10q26, (i.e., rs10490924, which is upstream of HTRA1 in LOC387715/ARMS2, and rs11200638) as D'=0.8, and all four possible haplotypes of the two SNPs were detected in the samples. Further, this same study reported that these two SNPs appear to contribute equal...
common in clinvar
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minor form is a slow metaboliser according to pharmgkb [PharmGKB:In-Depth This variant results in enzyme inactivity and is considered to be part of the %22slow metabolizer%22 group; part of the CYP2A6*2 haplotype.] [OMIM:?] [GWAS:Smoking behavior]
common in complete genomics
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rs6019 and rs6022 maternal smoking on PTD and gestational age. Compared with non-smoking mothers carrying rs6019(C) associated with significantly increased risk of PTD (OR(95% CI): 2.1(1.2-3.6) for GC; 5.7(2.1-15.0) for CC; p-interaction = 0.02 Polymorphism in maternal LRP8 gene is associated with fetal growth.
39 snps
(hide) Social anxiety disorder
Normal risk for anxiety disorders
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A study of patients with panic disorder or social anxiety disorder, both moderately heritable anxiety disorders, concluded that the rs140701(A) allele was associated with increased risk for both disorders. This SNP was actually part of a tightly linked haplotype A-A-G (for SNPs rs3794808, rs140701 and rs4583306, respectively) that had 1.7x increased risk for panic disorder (CI: 1.2-2.3).
complex; possible association with anxiety related behaviours
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In mice, the genetic locus best correlated to anxiety-related behaviour contains the 'regulator of G protein signaling 2' gene . In humans, SNPs in the equivalent RGS2 gene have now been studied to see if they are correlated to anxiety related disorders. In the first part of one study, 119 families including children underwent standard lab-based behavioural assessments of behavioural inhibition, defined as a heritable temperamental profile characterized by a tendency to be shy, avoident, and behaviourally restrained in situations that are novel or unfamiliar. Along with some other RGS2 SNPs, carriers of a rs4606(G) allele were 3 fold more likely to exhibit behavioural inhibition (CI: 1.31-6.84, p = 0.0026). In the second part of this study, 744 college undergraduates (228 men, 516 women) w...
2 snps
(hide) Speech
risk of speech development delay and/or impairment
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Speech development rs4431523, rs17236239 and significant associations (with P values from 0.01 to 5.0x10–5) between nonsense-word repetition and nine intronic SNPs (rs851715, rs10246256, rs2710102, rs759178, rs1922892, rs2538991, rs17236239, rs2538976, and rs2710117)
None
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Speech development rs4431523, rs17236239 and significant associations (with P values from 0.01 to 5.0x10–5) between nonsense-word repetition and nine intronic SNPs (rs851715, rs10246256, rs2710102, rs759178, rs1922892, rs2538991, rs17236239, rs2538976, and rs2710117)
None
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rs2710102, a common SNP in the CNTNAP2 gene, was found to be significantly associated (p<0.028) with a delayed onset of speech, as measured by the age at which a child speaks their first words, in children with autism. This effect is primarily seen in males, perhaps correlated with the 4-5x overrepresentation of males with autism compared with females. The confirmatory Stage 2 study was performed on 304 independent parent-child trios. However, the risk allele and the degree to which speech is delayed per genotype is unclear as published and awaits clarification by the authors. Speech development rs4431523, rs17236239 and significant associations (with P values from 0.01 to 5.0x10–5) between nonsense-word repetition and nine intronic SNPs (rs851715, rs10246256, rs2710102, rs759178,...
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news rs4431523 in CNTNAP2 were significantly associated with the inability of children with typical specific language impairment to process and repeat nonsense words NEJM Speech development rs4431523, rs17236239 and significant associations (with P values from 0.01 to 5.0x10–5) between nonsense-word repetition and nine intronic SNPs (rs851715, rs10246256, rs2710102, rs759178, rs1922892, rs2538991, rs17236239, rs2538976, and rs2710117)
higher risk of speech development delay and/or impairment
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Speech development rs4431523, rs17236239 and significant associations (with P values from 0.01 to 5.0x10–5) between nonsense-word repetition and nine intronic SNPs (rs851715, rs10246256, rs2710102, rs759178, rs1922892, rs2538991, rs17236239, rs2538976, and rs2710117)
5 snps
(hide) Split hand
common in complete genomics
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Split hand syndrome (or split hand and foot syndrome) is a developmental abnormality resulting in malformed or absent fingers and/or toes. There may be additional limb defects, such as absent tibias. Several different chromosomal regions have been implicated in this syndrome, among them * rs1124110 in the GALNT2 gene; the risk allele is G (reported as C by 23andMe) This variation is considered to be an autosomal dominant with low penetrance. In other words, the split hand defect will often skip generations, and most people who carry the risk variant of rs1124110 have normal hands and feet. There are known carriers of two risk alleles of rs1124110 who are normal, although other family members are affected. This pattern of inheritance indicates that more than one gene may be involved. [OMIM...
1 snp
(hide) Stroke
Lowest risk (13% of white women) of Atrial Fibrillation reported by 23andMe
The two atrial fibrillation SNPs mentioned by 23andMe are both normal. This causes the heart to form normally and gives the lowest risk of Atrial Fibrillation (quivering of the top part of the heart) that 23andMe reports. It also seems to lower the risk of Cardioembolic ischemic stroke (blocked blood flow to the brain) although 23andMe doesn't mention that. For European women, 23andMe reports this as a 13.0% risk, compared to the 15.9% average. The risk is higher for men. Based on many quality studies, and confirmed for Europeans and partly for Asians.
1.5x increased risk for CAD 1.5x higher risk for coronary artery disease
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rs1333049 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is most likely (C); the odds ratio associated with heterozygotes is 1.47 (CI 1.27-1.70), and for homozygotes, 1.9 (CI 1.61-2.24). This SNP has also been reported to have the highest association of any SNP studied in a subsequent experiment conducted with the resources of the German MI [Myocardial Infarction] Family Study. The initial studies were conducted on Caucasian populations. A subsequent study of Japanese and Korean patients has also found rs1333049 to be associated with increased coronary artery disease risk, with roughly similar odds ratios. '''Further reading (with comments)''' - A long-term study of a cohort of 76...
~1.5-3x increased risk for ischemic stroke
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rs2231137, also known as Val12Met, is a SNP in the ATP-binding cassette, sub-family G (WHITE), member 2 ABCG2 gene. The (G) allele encodes the Val. In a study of incident ischemic stroke during 14 years of follow-up in a population-based study of older adults known as the Cardiovascular Health Study (CHS), rs2231137 was associated with stroke in both white (hazard ratio, 1.46, CI: 1.05 - 2.03) and black (hazard ratio, 3.59, CI, 1.11 - 11.6) participants. The risk of ischemic stroke was higher in Val allele homozygotes than in Met allele carriers. The adjusted hazard ratio for Val allele homozygotes, compared with Met allele carriers, was 1.50 (90% CI, 1.06 to 2.12) in whites and 3.62 (90% CI, 1.11 to 11.9) in black participants (Table 4). [PharmGKB:Curated control size=7; M12 cases=6; PK=...
some risk linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil).
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
warfarin sensitivity (~2.5 mg/day)
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rs8050894, is located on chromosome 16 in the gene VKORC1. VKORC1 is the primary target of the drug warfarin (Coumadin), a commonly used oral anticoagulant. rs8050894 is one of several polymorphisms found in VKORC1 that is associated with specific warfarin doses (). Other polymorphisms in VKORC1 (rs7196161, rs9923231, rs9934438, rs2359612) are equally predictive of warfarin dose requirement in both European and Asian-descent individuals. Other polymorphisms found in the gene cytochrome P450 2C9 (CYP2C9) influence the metabolism of warfarin and have a smaller effect on warfarin dose. These polymorphisms are rs1799853 (CYP2C9*2) and rs1057910 (CYP2C9*3). In several hundred Europeans, no association was found between rs8050894 and risk for ischemic stroke. Genetic-based dosing in orthopedic p...
1.8x increased risk for high blood pressure
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rs4961 is a variation in the adducin 1 ADD1 gene, encoding a change from a glycine to a tryptophan, so it is also known as G460W or Gly460Trp. Originally, a study of 477 Italian patients indicated that carriers of one or two rs4961(T) alleles were at 1.8x increased risk for hypertension (CI: 1.32-2.43). This study also indicated that carriers of the risk (T) allele responded better to diuretics and sodium-restricted diets, in that they tended to lower their blood pressure by ~10 mmHg points compared to rs4961(G;G) homozygotes similarly treated. Subsequent studies have tended to confirm this association, and to extend it to risk for heart disease. They also have tended to confirm that risk allele carriers respond better to therapy. In a study of ~2200 Belgian patients, rs4961(T) carriers we...
Women have lower risk of Endometriosis but normal risk for Endometrial Cancer, and more cognitive impairment with age. Men have zero risk, but can pass this on to their daughters. This is the normal version of Estrogen Receptor 1 (alpha). It has more cognitive decline than the rare version, with old women only remembering half as much details on the East Boston Memory Test immediate recall test.
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rs9340799 is a SNP in the estrogen alpha receptor ESR1 gene, and it is also known as the -351A>G variant. Among women, rs8179176, rs9340799, rs1256065, and rs1256030 were associated with likelihood of developing cognitive impairment with ageing. In men, rs728524, rs1255998, and rs1256030 were associated with cognitive impairment. A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs9340799) and risk of ischemic stroke. A study of 702 cases with invasive endometrial cancer concluded that the less common alleles of SNP rs9340799 lowered risk for the disease. The odds ratio was 0.75 (CI: 0.60-0.93) for (A;G) and 0.53 (CI: 0.37-0.77) for (G;G) compared to rs9340799(A;A) individuals. Endometriosis Uterine Fibroids [PharmGKB:Curated SNP i...
Magnitude: 2
Frequency: 50.0%
Repute:Bad
References:77
Frequency: 50.0%
Repute:Bad
References:77
1.3x risk for Heart Attack. Normal risk for Abdominal Aortic Aneurysm and Brain Aneurysm. One copy of an SNP that increases risk of Myocardial Infarction (Heart Attack) and other Coronary Heart Disease. It has been shown that regularly eating raw vegetables and fruit can reduce the risk to the same level as people without this SNP. This SNP also has the normal medium risk of abdominal aortic aneurysm (weakened artery to abdomen and legs) or brain aneurysm (weakened artery to brain).
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This SNP, rs10757278, is one of several clustered together in a region of chromosome 9 that has been linked to increased risk for heart disease and potentially diabetes. The overall estimate of heart disease cases that may involve this SNP (or related ones nearby) is said to be 20-30%. The risk allele, rs10757278(G), shows an increased association for myocardial infarctions ('MI'; heart attacks) both in general and more specifically in so-called early onset MI. The odds ratio relative to rs10757278(A:A) 'noncarrier' individuals for rs10757278(G;G) individuals is 1.64 (CI: 1.47-1.82), and for carriers of one risk allele, i.e. rs10757278(A;G) individuals, 1.26 (CI: 1.16-1.36). For early onset MI, the odds are slightly higher; homozygote rs10757278(G;G) individuals have an odds ratio of 2.02 ...
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
0.86x decreased risk of Atrial Fibrillation This is the normal version which makes the heart form properly and makes people less likely to get Atrial Fibrillation (quivering of the top chambers of the heart caused by chaotic electrical signals) and less likely to have an Ischemic Stroke (blocked blood flow to the brain). But also check the other SNP nearby (rs10033464) which slightly affects Atrial Fibrillation too. 23andMe gave this a 4 star confidence rating as it has been heavily studied. It has been confirmed in Europeans and Asians.
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Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x. The results derived from a study of 78 Italians with atrial fibrillation (AF) and atrial flutter (AFL) agree with previously reported findings from the Icelandic study (), which also found that the rs2200733(T) was associated with AF/AFL disease. In 1,661 Icelandic ischemic stroke samples and two large European replication sets combined, rs2200733 was associated with cardioembolic stroke (CES) (odds ratio 1.54, p = 8.05 x 10e-9). rs2200733 even showed association to ischemic stroke that was not classified as cardioembolic stroke. rs2200733 and rs1003...
Magnitude: 1.9
Frequency: 82.3%
Repute:Good
References:13
Frequency: 82.3%
Repute:Good
References:13
0.92x decreased risk of Atrial Fibrillation and cardioembolic stroke. This is the normal version which makes the heart form properly and makes people slightly less likely to get Atrial Fibrillation (quivering of the top chambers of the heart caused by chaotic electrical signals) and less likely to have a cardioembolic stroke (blocked blood flow to the brain). But also check the other SNP nearby (rs2200733) which affects Atrial Fibrillation even more. 23andMe gave this a 4 star confidence rating as it has been heavily studied. It has been confirmed in Europeans.
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Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x. In 1,661 Icelandic ischemic stroke samples and two large European replication sets combined, rs10033464 was associated with cardioembolic stroke (CES) (odds ratio 1.27, p = 6.1 x 10e-4). rs2200733 and rs10033464 are strongly associated with AF in four cohorts of European descent. Variation in the 4q25 chromosomal locus predicts atrial fibrillation after coronary artery bypass graft surgery. Chromosome 4q25 variants and atrial fibrillation recurrence after catheter ablation. Common variants in KCNN3 are associated with lone atrial fibrillation. Associ...
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[PharmGKB:Non-Curated GWAS results: A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release (Initial Sample Size: 259 cases, 269 controls; Replication Sample Size: NR). This variant is associated with Stroke.] [GWAS:Stroke]
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linked to Cardiovascular Events Several CVD risk variants were identified: In women, the combination of F5 rs7542281 × THBD rs1042580, together with three single F5 SNPs, was associated with CVD events. Among men, PROC rs1041296, when combined with either ICAM1 rs5030341 or F5 rs2269648, was associated with total mortality. As a single variant, PROC rs1401296, together with the F5 Leiden mutation, was associated with ischemic stroke events. '''NOTE:''' SNPedia has raised a question with the authors of this paper (), in that it appears that their mention of 'rs1041296' is a typographical error, when they intended to refer to SNP rs1401296. Once a response is received from the authors, we will update the associated entries, and until then, ''Caveat Emptor''.
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients
Frequency: 30.1%
References:17
References:17
mixed evidence of increased risk for stroke 1.3x increased risk for stroke in an initial study, but failed to replicate in a followup.
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rs12425791 is one of 2 SNPs found near the NINJ2 gene on chromosome 12 associated with increased risk for both total stroke and ischemic stroke, based on a large study of four cohorts including both blacks and whites. The other (linked) SNP is rs11833579. Results of this 20,000+ person study suggested that each minor (risk) allele at these two SNPs increases the hazard ratio for total stroke about 1.31 (CI: 1.19 - 1.44) and for ischemic stroke by about 1.40 (CI: 1.27 - 1.56). The corresponding population attributable risks were 11 to 13% for total stroke and 14 to 17% for ischemic stroke, which is fairly high for this sort of SNP. Note: a meta-analysis totaling over 8,000 patients did not replicate any association between either rs12425791 or rs11833579 and ischemic (or incident) stroke. ...
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
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rs2230500 (V374I) and rs9943582 were significantly associated with stroke
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rs2234693 is a SNP upstream of the estrogen alpha receptor ESR1 gene, and is sometimes referred to as the -397T>C variation. rs2234693 rs9340799 and rs1256049 variations in ESR1 gene, in addition to the age of a woman, may predict the COH outcome in in vitro fertilization A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs2234693) and risk of ischemic stroke rs2234693(C;C)more frequent in African American schizophrenics (p=0.01 to 0.001). haplotype less common in schizophrenia rs2273206(T), rs2273207(G), rs2228480(G). Oestrogen receptor alpha gene haplotype and postmenopausal breast cancer risk: a case control study. Differential genetic effects of ESR1 gene polymorphisms on osteoporosis outcomes. Estrogen receptor alpha gene varia...
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients
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Although rs17611 was the only SNP to remain significant after multivariate analysis (odds ratio 0.585, p = 0.0037) in a study of 459 patients, ROC curve analysis did not show any contribution of this SNP to overall stroke risk. [OMIM:COMPLEMENT COMPONENT 5; C5]
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linked to Cardiovascular Events Several CVD risk variants were identified: In women, the combination of F5 rs7542281 × THBD rs1042580, together with three single F5 SNPs, was associated with CVD events. Among men, PROC rs1041296, when combined with either ICAM1 rs5030341 or F5 rs2269648, was associated with total mortality. As a single variant, PROC rs1401296, together with the F5 Leiden mutation, was associated with ischemic stroke events.
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rs9551963, also known as SG13S32, is an ALOX5AP gene SNP that has been defined as part of a haplotype potentially associated with risk for myocardial infarction or ischemic stroke. Details of this haplotype and several related studies are on the ALOX5AP page. Genetic effects in the leukotriene biosynthesis pathway and association with atherosclerosis. 5-Lipoxygenase activating protein (ALOX5AP) gene variants associate with the presence of xanthomas in familial hypercholesterolemia. Oxidative risk for atherothrombotic cardiovascular disease. The role of LTA4H and ALOX5AP genes in the risk for asthma in Latinos. ALOX5AP and LTA4H polymorphisms modify augmentation of bronchodilator responsiveness by leukotriene modifiers in Latinos.
Frequency: 43.5%
References:0
References:0
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients
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[PharmGKB:Non-Curated GWAS results: A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release (Initial Sample Size: 259 cases, 269 controls; Replication Sample Size: NR). This variant is associated with Stroke.] [GWAS:Stroke]
1.5x increased stroke risk
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A study of 639 Chinese stroke patients concluded that the rs966221(C) allele is associated with increased risk for atherothrombotic strokes (odds ratio 1.51, CI: 1.09-2.10) in this population.
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[PharmGKB:Non-Curated GWAS results: A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release (Initial Sample Size: 259 cases, 269 controls; Replication Sample Size: NR). This variant is associated with Stroke.] [GWAS:Stroke]
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association of the MMP-2 gene with the development of lacunar stroke. rs1030868, rs2241145, rs2287074, rs2287076, rs7201 showed a significant association with small vessel infarcts (p < 0.05) and rs7201:g.C was identified as an independent risk factor by multivariable logistic regression analysis
References:3
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rs17222842, also known as SG13S35, is an ALOX5AP gene SNP that has been defined as part of a haplotype potentially associated with risk for myocardial infarction or ischemic stroke. Details of this haplotype and several related studies are on the ALOX5AP page.
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients
2x higher stroke risk in Caucasian women
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rs6797312, a SNP in the neuroserpin SERPINI1 gene, was found to be associated with stroke risk in some populations but not others. In a study of 224 female patients (from 15-49 years old) equally divided between Caucasians and African-Americans, the rs6797312(A) allele was associated with higher risk (odds ratio 2.05, p=0.023) for early-onset ischemic stroke in Caucasians but showed no association in African-Americans.
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients
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The presence of an rs173686(C) allele has been linked to increased risk of a certain type of stroke, Intracranial Aneurysm, in a population of Dutch adults. A study of 240 Chinese Han nationality patients with at least one intracranial aneurysm and matched controls did not replicate this result. Note: the dbSNP sequence entry for this SNP represents the noncoding strand, and is thus the reverse complement compared to the SNP as referred to in .
0.10 decreased risk for brain edema after a stroke
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rs9951307is a SNP in the aquaporin-4 (AQP4) gene; the corresponding protein is the main water channel in the brain and is implicated in the development of brain edema after an ischemic stroke. A study of 41 patients with middle cerebral artery occlusion with and without severe brain edema found that rs9951307 was associated with severe brain edema (dominant model, p=0.01; OR, 0.10, CI: 0.02 to 0.49 for the protective (G) allele).
Magnitude: 0
Frequency: 89.2%
Repute:Good
References:3
Frequency: 89.2%
Repute:Good
References:3
common on affy axiom data
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Confirmation of genomewide association signals in Chinese Han population reveals risk loci for ischemic stroke. [PharmGKB:Non-Curated GWAS results: A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release (Initial Sample Size: 259 cases, 269 controls; Replication Sample Size: NR). This variant is associated with Stroke.] [GWAS:Stroke]
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rs4769874, also known as SG13S89, is an ALOX5AP gene SNP that has been defined as part of a haplotype potentially associated with risk for myocardial infarction or ischemic stroke. Details of this haplotype and several related studies are on the ALOX5AP page.
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Part of a haplotype linked to stroke affecting perhaps 5% of sickle cell anemia patients Sickle Cell Disease in the Post Genomic Era: A Monogenic Disease with a Polygenic Phenotype.
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
common in complete genomics
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stroke rs2069830(T) (frequency = 5%) protective among non-smokers (OR = 0.30, 95% CI=0.11-.082, p=0.02), but not among smokers (OR = 1.63, 95% CI=0.48-5.58, p=0.43)
normal risk
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A common SNP only in Asian populations, this SNP (also known as 1425G/A) and a close neighbor also in the PRKCH gene, rs3783799, have been associated with higher risk for subcortical silent brain infarction, a common form of stroke. In one study of ~1100 Japanese stroke patients, the odds ratio for carriers of the rs2230500(A) risk allele was reported as 1.40 (CI: 1.23-1.59, p=5x10e-7). A subsequent study reported the odds ratio for carriers of the (A) allele as 1.27 (CI: 1.09-1.48, p=0.0026) compared to individuals homozygous for rs2230500(G), based on studies of ~300 Japanese patients. rs2230500 (V374I) and rs9943582 were significantly associated with stroke Genetic association between the PRKCH gene encoding protein kinase Ceta isozyme and rheumatoid arthritis in the Japanese population...
Magnitude: 0
References:3
References:3
common for Caucasians on the 23andme platform
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rs17222814, also known as SG13S25, is an ALOX5AP gene SNP that has been defined as part of a haplotype potentially associated with risk for myocardial infarction or ischemic stroke. Details of this haplotype and several related studies are on the ALOX5AP page. rs17222814 on bifurcation intima-media thickness and alcohol consumption exceeding 30 grams per day
1 genoset 39 snps
(hide) Sudden Infant Death Syndrome
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
3x risk
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This position is referred to as the -1154 position in many VEGF-associated publications. The normal (or wild type) form of this SNP is a (G). The (A) form reduces the activity of this gene, resulting in less VEGF protein. Individuals with one or more rs1570360(A) alleles are reported to be at about a 3 fold higher risk of developing Sudden Infant Death Syndrome . A functional variant of vascular endothelial growth factor is associated with severe ischemic complications in giant cell arteritis. Analysis of vascular endothelial growth factor (VEGF) functional variants in rheumatoid arthritis. Association between functional haplotypes of vascular endothelial growth factor and renal complications in Henoch-Schonlein purpura. Polymorphisms in the vascular endothelial growth factor gene and brea...
common in clinvar
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rs7626962, also known as Ser1103Tyr or S1103Y, is a SNP in the cardiac sodium channel SCN5A gene. Although relatively common (for a rare allele; 10 - 20% of individuals) in those of African ancestry, in all populations the rs7626962(T) allele has been reported to increase the risk for cardiac issues such as long QT syndrome but also arrhythmias and even sudden infant death syndrome. The odds ratio for displaying signs of arrhythmia for anyone carrying a rs7626962(T) allele is reported as 8.7 (CI 3.2 - 23.9) ; as for sudden infant death syndrome, at least in African-ancestry populations, the odds ratio for the same allele is reported as 4.9, leading to an odds ratio of 24 for rs7626962(T;T) homozygotes. This variant meets the criteria published in 2013 by the ACMG regarding incidental findi...
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
complex; generally normal risk
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rs361525 is also known as the TNF-238 SNP, and occasionally the rs361525(A) allele is referred to as 238.2 (with the more common (G) allele being 238.1). This SNP in the tumor necrosis factor-alpha gene has been linked to a wide variety of conditions: * Breast cancer ** A large study of over 5,000 Caucasian women found that rs361525(A) allele carriers were at somewhat elevated risk for breast cancer compared to the (G;G) genotype, with an odds ratio per allele of 1.18, CI: 1.04-1.35, p(trend)= 0.008. ** However, a 2009 European study of 30,000 breast cancer cases, compared to 30,000 controls, found no association, or as they put it, 'persuasive evidence against an overall association between invasive breast cancer risk and (this SNP)'. * Graft versus host disease (GVHD) ** A study of ~100 ...
5 snps
(hide) Suicide
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rs7569963 is directly adjacent to CREB1. Associated with significantly (p = 0.005) increased chance of suicide in a study of 1447 citalopram users (male only subgroup, 539 in total). Two haplotypes (see below) also showed significant association with suicidality in the male subgroup. *rs2709376(C),rs2253206(A),rs7569963(A),rs7594560(T),rs4675690(C) - common haplotype, reduced chance of suicide in males, p = 0.004 *rs2709376(C),rs2253206(A),rs7569963(G),rs7594560(T),rs4675690(T) - increased chance of suicide in males, p = 0.009 [PharmGKB:Curated In a nested case-control study derived from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study this SNP in the CREB1 gene was associated with treatment-emergent suicidality among men with depression.]
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rs4675690 is in close proximity to CREB1, and adjacent to LOC151194. g2b2mh blog individuals with the TT genotype at rs4675690 (C/T) showed less disgust, but not happiness, desire or fear. T allele associated with increased chance of suicide (OR = 2.3, 95% CI 1.3-2.9, TT homozygotes vs CC homozygotes?) during the first 30 days (p > 0.05 after the first month) of citalopram treatment, in a study of 1447 citalopram users (male only subgroup, 539 in total). Two haplotypes (see below) also showed significant association with suicidality in the male subgroup. *rs2709376(C),rs2253206(A),rs7569963(A),rs7594560(T),rs4675690(C) - common haplotype, reduced chance of suicide in males, p = 0.004 *rs2709376(C),rs2253206(A),rs7569963(G),rs7594560(T),rs4675690(T) - increased chance of suicide in males...
normal
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This SNP, located in an intron of the GRIA3 gene (also known as AMPA3), has been linked in one study to increased thoughts of suicide in patients taking the anti-depressant drug citalopram. The increased risk is calculated to be 1.9x. If the individual is also carrying two rs2518224(C) alleles, i.e. is a rs2518224(C;C) homozygote, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6). [PharmGKB:Curated This SNP in the GRIA3 gene was associated with treatment-emergent suicidal ideation during citalopram therapy in a clinically representative cohort of outpatients with major depressive disorder. DNA samples from 1,915 participants were genotyped.]
normal
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This SNP, located in an intron of the GRIK2 gene, has been linked in one study to increased thoughts of suicide in patients using the anti-depressant drug citalopram. The risk is only seen for individuals carrying two rs2518224(C) alleles, i.e. the rs2518224(C;C) homozygotes. The odds ratio for these individuals is 8.2. If the individual also has at least one rs4825476(G) allele, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6). [PharmGKB:Curated This SNP in the GRIK2 gene was associated with treatment-emergent suicidal ideation during citalopram therapy in a clinically representative cohort of outpatients with major depressive disorder. DNA samples from 1,915 participants were genotyped.]
5 snps
(hide) Sun sensitivity
2-4x higher risk of sun sensitivity if part of risk haplotype. Increased risk of sunburns and freckles instead of tanning.
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rs1015362 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
2-4x higher risk of sun sensitivity if part of risk haplotype
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
2 snps
(hide) Systemic sclerosis
Magnitude: 2
Frequency: 21.2%
Repute:Bad
References:29
Frequency: 21.2%
Repute:Bad
References:29
2x increased risk of developing SLE; 1.6x increased risk of developing primary biliary cirrhosis; and 1.7x increased risk of developing Sjögren's syndrome
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rs10488631, a SNP located 3' of the IRF5 gene, has been reported as a possibly causative SNP for systemic lupus erthymatosus (SLE), based on a study of ~700 Swedish patients. The risk allele is rs10488631(C), with a reported odds ratio of 2.07 (CI: 1.63-2.62, p = 9x10e-10). The C allele is also associated with primary biliary cirrhosis, with each C increasing the odds about 1.6 times. Each C allele increases risk of Sjögren's syndrome by 1.7 times. SLE rs10488631 and rs7582694 [OMIM:INTERFERON REGULATORY FACTOR 5; IRF5] [GWAS:Systemic lupus erythematosus]
~normal risk
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rs6918698, a common SNP located in the promoter of the CTGF gene, has been linked to increased risk for systemic sclerosis (scleroderma) based on a study of 500 Caucasian patients. The odds ratio is 2.2 for (G;G) homozygotes (p<0.001). The reason that the (C) allele appears to be protective is thought to be due to decreased CTGF activity. [OMIM:CONNECTIVE TISSUE GROWTH FACTOR; CTGF]
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[GWAS:Systemic sclerosis]
normal
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rs6457617 has been reported in a large study to be associated with rheumatoid arthritis. This SNP is reported to be the most statistically significant of many SNPs similarly located in the MHC region. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 2.36 (CI 1.97-2.84), and for homozygotes, 5.21 (CI 4.31-6.30). [GWAS:Rheumatoid arthritis]
normal
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rs2834167 is a SNP in the interleukin-10 receptor 2 IL10RB gene. In a study of Japanese patients, rs2834167(A;A) individuals were at increased risk for diffuse cutaneous systemic sclerosis (odds ratio 2.67, p = 0.0018). [OMIM:?]
normal
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CPMC uses this to indicate increased risk of Systemic lupus erythematosus. [GWAS:Systemic lupus erythematosus]
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
7 snps
(hide) Taste
Able to taste bitterness.
Normal tasting ability for bitterness. This makes turnip, cabbage, brussels sprouts, broccoli, and other cruciferous vegetables taste more interesting and less horribly bland. Coffee and dark beers also tastes more bitter. You can taste propylthiouracil (PROP), PTC, and related chemicals. On the other hand, you can't taste the unpleasant bitterness of the tropical fruit from the Bignay tree, it will taste sweet to you. You probably eat healthier.
Can taste bitter. Normal tasting ability for bitterness. This makes turnip, cabbage, brussels sprouts, broccoli, and other cruciferous vegetables taste more interesting and less horribly bland. Coffee and dark beers also tastes more bitter. You can taste propylthiouracil (PROP), PTC, and related chemicals. On the other hand, you can't taste the unpleasant bitterness of the tropical fruit from the Bignay tree, it will taste sweet to you. You probably eat healthier.
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rs713598 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs713598(G) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs713598(C), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs10246939(C) and one rs1726866(C) allele since, along with rs713598(G), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others ta...
Magnitude: 0.1
Frequency: 19.5%
References:10
Frequency: 19.5%
References:10
can taste bitter
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rs10246939 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs10246939(C) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs10246939(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs1726866(C) allele since, along with rs10246939(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to oth...
can taste bitter
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rs1726866 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs1726866(C) allele is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs1726866(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs10246939(C) allele since, along with rs1726866(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others taste far less bitter to you. (C;C)...
common in complete genomics
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Influences tasting ability. This blog entry discusses the research. the rare T allele of rs307377(T) (R757C) in TAS1R3 led to a doubling of umami ratings of 25 mmol MPG/L. Other suggestive SNPs of TAS1R3 include the A allele of A5T and the A allele of R247H, which both resulted in an approximate doubling of umami ratings of 200 mmol MPG/L
1 genoset 4 snps
(hide) Tay-Sachs disease
normal
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This SNP is associated with a change in the protein encoded by the HEXA gene, which leads to a false positive blood test for Tay-Sachs Disease. In other words, the blood test from an individual with an i4000440(A) allele will indicate the person is a carrier for Tay Sachs disease, even though this SNP is not actually one that leads to the disease. Note however that the person may still carry (on their other chromosome 15) a 'true' Tay Sachs causing allele. rs138058578
normal
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This SNP is associated with a change in the protein encoded by the HEXA gene, which leads to a false positive blood test for Tay-Sachs Disease. In other words, the blood test from an individual with an i4000442(A) allele will indicate the person is a carrier for Tay Sachs disease, even though this SNP is not actually one that leads to the disease. Note however that the person may still carry (on their other chromosome 15) a 'true' Tay Sachs causing allele. rs121907970
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs76173977 is a mutation in the 9th intron (IVS9) of the HEXA gene, and it has been reported as one of the more common mutations seen in non-Jewish Caucasians which can lead to Tay-Sachs disease when present in two copies or when combined with another Tay-Sachs mutation. The best write-up of this mutation is found in OMIM. Note that 23andMe refers to this SNP as i4000438.
common in clinvar For 23andMe users, this is the normal genotype. However see also Rs28940871(G;G)
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This position appears to have been flipped between b36 and b37. Extra scrutiny is warranted. rs28940871, also known as Leu451Val, L451V, or C1351G, is a mutation in the HEXA gene. Some variations of this gene are associated with Tay-Sachs disease. In a population of Iraqi Jews, this SNP was found in 21 of 62 Tay-Sachs disease carriers (33.9%) and in 0 of 100 noncarriers. The authors estimated that this SNP originated sometime between 1519 BC and 635 AD, with 442 BC as the best estimate (+/- 1,000 years). The Iraqi Jewish community started around 586 BC when the Babylonian king Nebuchadnezzar deported 10,000 to 40,000 of the Jews from the kingdom of Judea to Babylon. This was probably the time of separation of the Iraqi Jews from the rest of the Jewish people. OMIM 23andMe reports the risk ...
11 snps
(hide) Testicular cancer
3x lower odds of testicular cancer risk for men
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Testicular germ cell tumor risk I('TGCT'; i.e. testicular cancer risk) was increased 3x per copy of the major (T) allele at rs3782179 and rs4474514 (OR = 3.08, CI: 2.29–4.13; OR = 3.07, CI = 2.29–4.13, respectively), based on a genome-wide scan of 277 primarily Caucasian TGCT cases and 919 controls. Men who have two copies of the common version of the c-KIT ligand KITLG gene have a 4.5-fold higher risk of testicular cancer than men who have two copies of the less common or minor version of the gene. https://www.23andme.com/you/community/thread/7837/ The original study was also only done in 277 people with the disease and 900 controls, so it's a very small study. [OMIM:?]
reduced risk of testicular cancer in men see discussion at rs995030
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23andMe blog each rs4624820(G) increases the odds of testicular cancer by 2.5x. <p><br> As reported by the CPMC, relative to men who are rs995030(A;A), men who are rs995030(A;G) have a 0.38 relative risk, and those who are (G;G) have a 0.15 relative risk. Association of genetic markers within the KIT and KITLG genes with human male infertility. Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancer. [OMIM:?] [GWAS:Testicular germ cell tumor]
3x increased testicular cancer risk for men
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Testicular germ cell tumor risk I('TGCT'; i.e. testicular cancer risk) was increased 3x per copy of the major (A) allele at rs3782179 and rs4474514 (OR = 3.08, CI: 2.29–4.13; OR = 3.07, CI = 2.29–4.13, respectively), based on a genome-wide scan of 277 primarily Caucasian TGCT cases and 919 controls. Men who have two copies of the common version of the c-KIT ligand KITLG gene have a 4.5-fold higher risk of testicular cancer than men who have two copies of the less common or minor version of the gene. SNPs from the same gene were also implicated in testicular cancer risk in a study of 730 cases and 1,435 controls from the UK and replicating associations in a further 571 cases and 1,806 controls. A second independent locus within DMRT1 is associated with testicular germ cell tumor...
1.3x increased risk for testicular cancer
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A study of 577 cases of testicular germ cell tumors, the most common testicular cancer in young men, concluded that the rs2059693(T) allele increased risk. Among Caucasians, the odds ratio for the rs2059693(C;T) genotype was 1.33 (CI: 1.04-1.71), and for the (T;T) genotype, 1.60 (CI: 1.01-2.52, p(trend) = 0.008). The association with rs2059693 was even stronger for nonseminomas, and for teratomas and teratocarcinomas in particular (N = 58; (C;T) odds ratio 1.63, CI: 0.89-2.99; (T;T) odds ratio 4.54, CI: 2.00-10.3, p(trend) = 0.0008).
>3x increased testicular cancer risk for men
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Testicular germ cell tumor risk I('TGCT'; i.e. testicular cancer risk) was increased 40% per copy of the major allele (C) at rs4324715 and rs6897876 (OR = 1.37, CI: 1.14–1.64; OR = 1.39, CI: 1.16–1.66, respectively), based on a genome-wide scan of 277 primarily Caucasian TGCT cases and 919 controls. Men who have two copies of the common version of the sprouty 4 SPRY4 gene have a 1.5-fold higher risk of testicular cancer than men who have two copies of the less common or minor version of the gene. [doi|10.1038/ng.393]
Normal risk of testicular cancer.
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Testicular germ cell tumor risk I('TGCT'; i.e. testicular cancer risk) was increased 40% per copy of the major (T) allele at rs4324715 and rs6897876 (OR = 1.37, CI: 1.14–1.64; OR = 1.39, CI: 1.16–1.66, respectively), based on a genome-wide scan of 277 primarily Caucasian TGCT cases and 919 controls. Men who have two copies of the common version of the sprouty 4 SPRY4 gene have a 1.5-fold higher risk of testicular cancer than men who have two copies of the less common or minor version of the gene. [doi|10.1038/ng.393]
increased testicular cancer risk for men
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23andMe blog each rs4624820(A) increases the odds of testicular cancer by 1.37x [OMIM:?] [GWAS:Testicular germ cell tumor]
normal
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Testicular cancer patients may be treated with bleomycin, a cytotoxic drug that is essential component of chemotherapy regimens for this cancer, officially known as disseminated testicular germ-cell cancer (TC). rs1050565 is a SNP in the BLMH gene. This gene encodes a protein that can inactivate bleomycin. Based on a study of 300 TC patients treated with bleomycin, a testicular cancer patient with a rs1050565(G;G) genotype has an odds ratio of 4.97 (CI: 2.17 - 11.39) for TC-related death compared to (A;G) or (A;A) genotypes. The rs1050565(G;G) genotype also shows a higher prevalence of early relapses. [PharmGKB:Curated Testicular germ cell cancer patients carrying the homozygous G/G allele of this variant showed reduced survival and higher prevalence of early relapses after treatment with...
common in complete genomics
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23andMe blog each rs210138(G) was found to increase the odds of testicular cancer by 1.5x [OMIM:?] [GWAS:Testicular germ cell tumor]
9 snps
(hide) Thiopurine methyltransferase deficiency
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
3 snps
(hide) Thrombocytopenia
MI risk, aspirin resistance 23andMe blog lower odds of early stent thrombosis
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The 'A2' allele of the platelet specific alloantigen system is encoded by rs5918(C), and it has been implicated as increasing the risk of myocardial infarctions, heart disease, and resistance to blood-thinning benefits of aspirin. On its own, the A2 allele is implicated especially in early onset heart disease ; in combination with the 4G allele of the PAI1 gene, rs1799889, the increased risk of myocardial infarction in a Finnish study population was 4 fold higher (odds ratio = 4.5, p=0.001), particularly in males (odds ratio = 6.4, p=0.0005) . Olympic skater Sergei Grinkov, who had this risk factor, died of a heart attack at age 28. A2 allele carriers also appear to be relatively resistant to the anti-thrombotic (i.e. anti-clotting) actions normally associated with aspirin] use. A protecti...
common on affy axiom data
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Carriers of the C allele at rs6139030 have a higher risk of developing thrombocytopenia when treated with interferon. Hepatitis C Treatment Side Effects [GWAS:None]
3 snps
(hide) Thyroid cancer
2.6x increased thyroid cancer risk
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Each A at rs965513 increased the odds of thyroid cancer by 1.75 times. Each T at rs944289 increased the odds of thyroid cancer by 1.37 times. A genoset, Gs137, has also been created in SNPedia to represent the increased risk reported for carriers of both variants. See also: 23andMe blog [PharmGKB:Non-Curated GWAS results: Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations. (Initial Sample Size: 192 cases, 37,196 controls; Replication Sample Size: 432 cases, 1,727 controls); (Region: 14q13.3; Reported Gene(s): NKX2-1; Risk Allele: rs944289-T); (p-value= 0.000000002).This variant is associated with Thyroid cancer.] [OMIM:THYROID CARCINOMA, PAPILLARY]
1.7x increased thyroid cancer risk
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rs965513 is located at 9q22.23 approximately 57 kb from the FOXE1 locus. The rs965513 SNP is associated with papillary and follicular thyroid cancer. The major allele is G and the minor is A. The risk allele is A. Each A at rs965513 increased the odds of thyroid cancer by 1.75 times. ==Clinical Picture== In a given year, roughly 5 in 100,000 males and 14 in 100,000 females will develop differentiated thyroid carcinoma (DTC). It is the most common endocrine cancer and rates are steadily rising, though this is likely due to increased detection. Significant risk factors for developing DTC include radiation exposure during childhood whether during treatment of childhood cancers or from environmental exposure, family history, occupational exposures, and possibly hepatitis-C related chronic hepa...
Possible elevated thyroid cancer risk After combining the results, three variants were shown to associate with thyroid cancer: rs966423 on 2q35 (OR = 1.34; P(combined) = 1.3 × 10(-9)), rs2439302 on 8p12 (OR = 1.36; P(combined) = 2.0 × 10(-9)) and rs116909374 on 14q13.3 (OR = 2.09; P(combined) = 4.6 × 10(-11)), a region previously reported to contain an uncorrelated variant conferring risk of thyroid cancer.
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[GWAS:None]
1.5x increased risk for thyroid cancer
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rs1867277, also known as -283G>A, is a SNP upstream of the FOXE1 gene. Based on ~1,000 thyroid cancer patients (and an equal number of controls), a per allele odds ratio of 1.49 (CI: 1.30-1.70, p=5.9x10e-9) was found for the rs1867277(A) allele. This allele is thought to be a causal variant.
normal
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rs2145418 is a SNP in the chromosome 1p12-13 region. In a case-control association study in a Spanish population, rs2145418 was associated with increased risk for thyroid cancer. rs2145418(G;T) heterozygotes had an odds ratio of 5.0 (CI: 2.85 - 8.83), while (G;G) homozygotes had an increased odds ratio of 9.2 (CI: 4.50 - 21.6), with reported significance of p < 0.0001.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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NOTE: the OMIM entry cited below refers to a somatic mutation, not a germline SNP [OMIM:THYROID CARCINOMA, FOLLICULAR, SOMATIC]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs28934576, also known as Arg273His or R273H, is a SNP in the p53 TP53 tumor suppressor gene. The minor allele is denoted as pathogenic (causal) in ClinVar. The rare rs28934576(A) allele is associated with predisposition to cancer in the form of Li-Fraumeni syndrome 1. Germline p53 Mutation in a Case of Li-Fraumeni Syndrome Presenting Gastric Cancer. A germline missense mutation CGT (Arg, wild type) to CAT (His) substitution at codon 273 of the p53 gene, causing Li-Fraumeni Syndrome with a gastric cancer in a Japanese. PCR direct sequencing analysis revealed a germline missense mutation in exon 8, causing a substitution of CAT (His) for CGT (Arg). See also OMIM 191170.20 This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencin...
8 snps
(hide) Torsion dystonia
common/normal
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23andMe tests for one mutation that causes torsion dystonia: i4000446, also known as deltaE302 (the risk genotype is a deletion) The rest of the world knows this SNP as rs80358233.
2 snps
(hide) Tourette syndrome
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[GWAS:Tourette syndrome]
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[GWAS:Tourette syndrome]
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[GWAS:Tourette syndrome]
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[GWAS:Tourette syndrome]
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[GWAS:Tourette syndrome]
Normal risk of developing restless legs syndrome
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rs9357271, a SNP located in the BTBD9 gene region, has been linked to a lower frequency of restless legs syndrome, a common sleep disorder, with an overall odds ratio of 0.63 (CI: 0.52-0.75) for the (C) minor allele. This SNP may also be associated with Tourette syndrome (TS), particularly TS without obsessive-compulsive disorder, based on a study of ~600 patients. [PharmGKB:Curated In replicated GWAS case-control studies of Caucasian(European and French-Canadian) familial and sporadic RLS, the T allele of rs9357271 was significantly associated with Restless Legs Syndrome.] [OMIM:RESTLESS LEGS SYNDROME, SUSCEPTIBILITY TO, 6] [GWAS:None]
Frequency: 77.0%
References:1
References:1
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[GWAS:Tourette syndrome]
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[GWAS:Tourette syndrome]
8 snps
(hide) Trimethylaminuria
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[OMIM:?]
common in clinvar
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rs1736557, also known as Val257Met, is a SNP in the FMO3 gene. It has been linked to trimethylaminuria; see variant .0002, OMIM 136132. [OMIM:?]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in clinvar
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rs61753344 is a SNP in the FMO3 gene. It has been reported in both homozygous and heterozygous forms to potentially be linked to trimethylaminuria; in the homozygous form, it has also been linked to tachycardia and severe hypertension after eating cheese (which contains tyramine) and after using nasal epinephrine. [OMIM:?]
4 snps
(hide) Tuberculosis
1.2 - 1.8x increased tuberculosis risk
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rs3764880 is a SNP in the TLR8 gene, located on the X chromosome. rs3764880 is also known as Met1Val. A study of both Indonesian and Russian tuberculosis patients (and controls) concluded that the minor (A) allele of rs3764880 was associated with increased risk for tuberculosis. In the Indonesian population of 375 patients, the odds ratio was 1.8 (CI: 1.2–2.7); in the Russian population of 1,837 patients, the odds ratio was 1.2 (CI: 1.02–1.48); the combined evidence for association was p = 1.2×10e?3 – 6×10e?4. Note that the association was found primarily in males (although also to a lesser extent in homozygous females), presumably due to the presence of only one X chromosome in males. A functional toll-like receptor 8 variant is associated with HIV disease rest...
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[GWAS:Tuberculosis]
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[GWAS:Tuberculosis]
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[GWAS:Tuberculosis]
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[GWAS:Tuberculosis]
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[GWAS:Tuberculosis]
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[GWAS:Tuberculosis]
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[GWAS:Tuberculosis]
normal risk
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rs1024611, also known as the -2578A>G SNP due to its position in the promoter of the monocyte chemoattractant protein-1 MCP-1 CCL2 gene, influences the production of its corresponding protein, a chemokine involved in inflammatory responses. In a study focusing on 679 apparently healthy siblings of people with premature heart disease, investigators found that carriers of an rs1024611(C) allele - oriented as in dbSNP, not as published - independently predicted the risk of exercise induced ischemia in general. The odds ratio was reported to be 1.86 (CI: 1.14-3.04, p=0.014), regardless of race, age, sex and other factors. However, it is not clear if this risk carries over to individuals who lack siblings with heart disease. discussed in the 23andMe blog as being relevant to HIV rs1024611 is...
common on affy axiom data
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23andMe blog rs8177374(T) less susceptible to infection with malaria, tuberculosis, bacteremia and pneumococcal disease. [PharmGKB:Curated In a case-control study of 6,106 individuals from the UK, Vietnam and several African countries with invasive pneumococcal disease, bacteremia, malaria and tuberculosis the heterozygous carriage of this variant was associated independently with all four infectious diseases in the different study populations. Further this study found a protective effect of S180L heterozygosity against these infectious diseases. A second study could not confirm this association.] [OMIM:TIR DOMAIN-CONTAINING ADAPTOR PROTEIN; TIRAP]
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associated with genetic susceptibility to tuberculosis in West Africa Variants in the SP110 gene are associated with genetic susceptibility to tuberculosis in West Africa. Polymorphisms in IL-1beta, vitamin D receptor Fok1, and Toll-like receptor 2 are associated with extrapulmonary tuberculosis. SP110 gene polymorphisms and tuberculosis susceptibility: A systematic review and meta-analysis based on 10 624 subjects. [OMIM:NUCLEAR BODY PROTEIN SP110; SP110]
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tuberculosis [OMIM:NUCLEAR BODY PROTEIN SP110; SP110]
12 snps
(hide) Tuberous sclerosis
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
common in clinvar
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rs45483392 is a SNP in the TSC2 gene on chromosome 16, associated with tuberous sclerosis in an autosomal dominant manner. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 191092.0009 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs45515894 is a SNP in the TSC2 gene on chromosome 16, associated with tuberous sclerosis in an autosomal dominant manner. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 191092.0017 Three independent mutations in the TSC2 gene in a family with tuberous sclerosis. [OMIM:?]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
common in clinvar
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rs45517259 is a SNP in the TSC2 gene on chromosome 16, associated with tuberous sclerosis in an autosomal dominant manner. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 191092.0013 [OMIM:?]
3 snps
(hide) Type-1 diabetes
increased risk for celiac disease increased resistance to bacterial infections
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rs3184504 is a nonsynonymous SNP in the SH2B3 gene, and it is also known as R262W. In a recent (2008) study of non-HLA SNP associations of 1600+ celiac disease patients, this SNP was considered one of the most significant. The odds ratio for the minor allele was 1.19 (CI:1.10-1.30, p=1.33x10e-7). rs653178, another SNP in strong linkage disequilibrium (r<sup>2</sup>>0.99) with rs3184504, was also associated with celiac disease. associated with type-1 diabetes 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 23andMe blog blood pressure Pharmacogenetic implications for eight common blood pressure-associated...
Magnitude: 2.5
Frequency: 38.9%
Repute:Bad
References:118
Frequency: 38.9%
Repute:Bad
References:118
increased risk for type-2 diabetes
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rs13266634 is a SNP in the zinc transporter protein member 8 SLC30A8 gene that has primarily been associated with type-2 diabetes in several studies. This SNP is also known as the Arg325Trp or R325W variant; the (C) allele encodes the arginine (R), and the (T) allele encodes the tryptophan (W). significantly associated p = 0.0073; in 1,630 Japanese subjects with type-2 diabetes and in 1,064 controls The major alleles of the SLC30A8 SNP rs13266634 and the HHEX SNP rs7923837 associate with reduced insulin secretion, but not with insulin resistance. 46% of European non-diabetic offspring of type-2 diabetes patients are rs13266634(C;C) homozygotes; they are diabetes-prone and characterised by a 19% decrease in first-phase insulin release following an intravenous glucose load. * Note: this SNP,...
Avg. fasting Plasma Glucose 5.18 mmol/L (93 mg/dl). Slightly higher blood glucose. Fasting Plasma Glucose is the amount of sugar in your blood when you wake up. It's required to power your body, but too much is very bad for you. Fasting plasma glucose between 5.6 mmol/L and 6.9 mmol/L (101 – 125 mg/dl) is considered pre-diabetes. Fasting plasma glucose higher than 7 mmol/L (126 mg/dl) is considered diabetes.
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rs560887, p = 4 x 10(-7)) *654 normoglycemic subjects, replicated in 9,353 subjects *fasting plasma glucose (FPG) (beta = -0.06 mmol/l per A-allele, combined p = 4 x 10(-23)) and with pancreatic beta-cell function (Homa-B model, combined p = 3 x 10(-13)) in three populations; however it was not associated with type 2 diabetes risk. (ageing) Blood Glucose [PharmGKB:Non-Curated Phenotype 1: In a meta-analysis of 21 GWAS cohorts followed by analysis in additional individuals, this SNP was found to be associated with fasting glucose level. Study size: 119,169. Significance metric(s): p = 8.7 x 10(-218). Phenotype 2: In the same study, this SNP was found to be associated with HOMA-B (homeostasis model assessment of beta-cell function). Study size: 94,839. Significance metric(s): p = 1.5 x 10(-...
Much lower 0.15x risk of Type 1 Diabetes. According to 23andMe, this SNP greatly reduces your risk of Type 1 Diabetes. Type 1 Diabetes is an autoimmune disease where your immune system attacks your own body's insulin producing cells in the pancreas, preventing your blood sugar from being able to enter cells that need energy. This has been verified for white people. 23andMe originally wanted to use rs9272346 instead, but it was deemed unreliable.
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This is one of the SNPs that 23andMe uses for Type 1 diabetes. According to 23andMe, this SNP changes your risk of Type 1 Diabetes. That is an autoimmune disease where your immune system attacks your own body's insulin producing cells in the pancreas, preventing your blood sugar from being able to enter cells that need energy. This has been verified for white people. 23andMe originally wanted to use rs9272346 instead, but it was deemed unreliable. [GWAS:Chronic lymphocytic leukemia]
Increased risk of Multiple Sclerosis.
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rs3129934 is a SNP near the HLA-class II region that may be associated with several autoimmune diseases. In a study of two cohorts (Spanish and American multiple sclerosis patients, each numbering several hundred), rs3129934 was the SNP most associated with increased risk for multiple sclerosis. The odds ratio was 3.3 (CI: 2.3 - 4.9, p = 9 x 10e-11). Seven other SNPs were also identified in this study as associated with increased risk for MS. associated with type-1 diabetes. 1.6x risk of type-1 diabetes? 23andMe uses rs9273363 instead of rs3129934 in its reports on type 1 diabetes risk. This SNP was formerly used as a proxy for rs9272346, with this explanation: 'Note: the 2007 Wellcome Trust paper reported a strong association between type 1 diabetes and the SNP rs9272346. Our quality cont...
1.33x increased risk of Ulcerative Colitis, but much lower Type 1 Diabetes risk. This raises the risk of Ulcerative Colitis (according to 23andMe), but also greatly lowers the risk of Type 1 Diabetes. It may also affect other autoimmune diseases.
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A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ancestry, concluded that this SNP and several others were associated with altered risk for the disease. [PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 6p21.32; Reported Gene(s): BTNL2, HLA-DRA, HLA-DRB5, HLA-DRB1, HLA-DQA1, HLA-DQB1; Risk Allele: rs2395185-?); (p-value= 0.0000000000000001).This variant is associated with Ulcerative colitis.] [OMIM:?] [GWAS:Ulcerative colitis]
1.5x increased risk for multiple sclerosis
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The (C) allele of rs6897932, located in the alternatively spliced exon 6 of IL7RA gene and encoding the amino acid threonine rather than isoleucine at amino acid position 244, is associated with a slight increase (18%) in risk of developing multiple sclerosis. [PMID 17660817; Nature Genetics 39, 1083 - 1091 (2007) SG Gregory et al.] Note that the (C) allele is the most common at this position in all known populations and influences the ratios of the alternative isoforms (membrane bound and soluble) of the gene. blog post giving perspective on the significance of this snp a significant risk factor for multiple sclerosis in four independent (overall P = 2.9 x 10(-7)) influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silenc...
Magnitude: 1.5
Frequency: 47.8%
Repute:Bad
References:9
Frequency: 47.8%
Repute:Bad
References:9
1.34x risk of developing Type-1 diabetes
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rs11171739 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.34 (CI 1.17-1.54), and for homozygotes, 1.75 (CI 1.48-2.06). In an expanded follow-up study of >6,000 controls and 6,000 patients, in which rs2292239 was ultimately chosen to replace the nearby rs11171739 originally determined to be associated with type-1 diabetes, the heterozygote odds ratio for SNP rs11171739 was recalculated to be 1.22 (CI 1.17–1.29). [PharmGKB:Non-Curated A genome-wide association study in 2,000 individuals for each of 7 major diseases and a shared set of 3,000 controls found an association of this SNP with type 1 diabetes.] [GWAS:Type 1 diabetes]
Slightly increased risk for multiple autoimmune diseases, such as type-1 diabetes Higher risk of type-1 diabetes.
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rs763361, also known as Gly307Ser, is a SNP in the immune response CD226 gene. The rs763361(T) allele (in dbSNP orientation) encodes the Ser. Based on multiple studies (by one group) now totaling over 2,000 patients, the rs763361(T) allele is associated with increased risk for multiple autoimmune diseases, including type-1 diabetes (p = 3 x 10e-9), multiple sclerosis (p = 4 x 10e-4), and possibly rheumatoid arthritis (p = 0.017). Based on tag SNP analysis, the authors conclude that this SNP could be the causal variant. Tested in a large multiple sclerosis data set consisting of 2369 trio families, 5737 cases and 10 296 unrelated controls, SNP rs763361 was associated with disease risk (p = 5.4 x 10e-8) [PharmGKB:Non-Curated GWAS Results: Robust associations of four new chromosome regions f...
increased risk for auto-immune diseases
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The rs3087243 SNP is also known in the literature as the CT60 G>A or the +6230G>A polymorphism, and it is located in the CTLA4 gene. In Asian (Japanese) populations, the presence of an rs3087243(G) allele represents a 1.3 fold increased risk of autoimmune thyroid disease, and for those with autoimmune thyroid disease, a 1.5 fold increased risk of type-1 diabetes. However, in individuals without autoimmune thyroid disease, no association was seen between this SNP and type-1 diabetes. The authors speculate that earlier studies may have reported associations between this SNP and type-1 diabetes that were actually primarily based on the association with autoimmune thyroid disease. This same SNP, rs3087243, has also been implicated as a (minor) risk factor for developing rheumatoid arthri...
For type-1 diabetics, 1.6x increased nephropathy risk
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rs4496877 is a SNP near the NOS3 gene. Several Type-1 diabetes patients pools, totaling over 2,000 patients, plus a meta-analysis were involved in a study concluding that in such patients, the rs4496877 was associated with higher risk for nephropathy. The odds ratio associated with rs4496877(T) was 1.26 (p = 0.002, CI: 1.08-1.47). A proxy for this SNP (pairwise linkage of 0.96) is rs1800783.
Frequency: 8.0%
References:4
References:4
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[OMIM:?] [GWAS:Type 1 diabetes]
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type-1 diabetes rs876498 (P=1.0x10(-4))
normal
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rs3194051, one of several SNPs in the IL7R gene, has been reported in a large study to be associated with type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.12 (CI 1.05–1.19). Study of the association between the CAPSL-IL7R locus and type 1 diabetes. Use of a genetic isolate to identify rare disease variants: C7 on 5p associated with MS. Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes. Analysis of 55 autoimmune disease and type II diabetes loci: further confirmation of chromosomes 4q27, 12q13.2 and 12q24.13 as type I diabetes loci, and support fo...
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[GWAS:None]
Frequency: 13.3%
Repute:Bad
References:27
Repute:Bad
References:27
1.94x risk of type-1 diabetes
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rs17696736 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.34 (CI 1.16-1.53), and for homozygotes, 1.94 (CI 1.65-2.29). In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.22 (CI 1.15–1.28). [PharmGKB:Curated GWAS results: Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample Size: 6,225 cases, 6,946 controls, 3,064 trios); (Region: 12q24.13; Reported Gene(s): C12orf30; Risk Allele: rs17696736-G); (p-value= 0.000000000000000006).This variant ...
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[PharmGKB:Non-Curated Follow up analysis of genome-wide association data identifies novel loci for type 1 diabetes. (Initial Sample Size: 563 cases, 1,146 controls, 483 case-parents trios; Replication Sample Size: 636 families, 3,303 cases, 4,673 controls); (Region: 21q22.3; Reported Gene: UBASH3A; Risk Allele: rs9976767-C) This variant is associated with Type 1 diabetes.] [GWAS:Type 1 diabetes]
somewhat increased risk for type-1 diabetes and allergic asthma
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rs3804100, also known as 1350T/C, is a SNP in the toll-like receptor 2 TLR2 gene. A study of 700 T1D children, 357 nuclear families with T1D children and 796 children from the 'Environment and Childhood Asthma' study concluded that both type-1 diabetes and allergic asthma were significantly associated with the rs3804100(T) allele.
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[PharmGKB:Non-Curated Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample Size: 6,225 cases, 6,946 controls, 3,064 trios); (Region: 22q13.1; Reported Gene: C1QTNF6; Risk Allele: rs229541-T) This variant is associated with Type 1 diabetes.] [OMIM:DIABETES MELLITUS, INSULIN-DEPENDENT; IDDM] [GWAS:Type 1 diabetes]
Frequency: 21.6%
References:3
References:3
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[PharmGKB:Non-Curated Follow up analysis of genome-wide association data identifies novel loci for type 1 diabetes. (Initial Sample Size: 563 cases, 1,146 controls, 483 case-parents trios; Replication Sample Size: 636 families, 3,303 cases, 4,673 controls); (Region: 9p24.2; Reported Gene: GLIS3; Risk Allele: rs10758593-A) This variant is associated with Type 1 diabetes.] [GWAS:Type 1 diabetes]
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rs1129456 is a SNP in the gremlin 1 GREM1 gene. An analysis combining several populations (~1,300 patients) indicated that the rs1129456(T) allele is associated with greater risk of nephropathy (odds ratio 1.69, CI: 1.36 - 2.11) among type-1 diabetes patients.
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Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. [PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs2816316-C).] [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 7; CELIAC7] [GWAS:Celiac disease] [GWAS:Celiac disease]
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associated with type-1 diabetes Type 1 Diabetes
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[GWAS:Type 1 diabetes]
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Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. Fine mapping the TAGAP risk locus in rheumatoid arthritis. [PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs1738074-A).] [OMIM:CEL...
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This SNP is associated with a higher risk of liver injury in patients taking the nonsteroidal anti-inflammatory drug lumiracoxib, which has been withdrawn from most markets.
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[GWAS:Type 1 diabetes]
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The association between type-1 diabetes and rs5215 is mentioned as being replicated in ; there is also a 90% correlation between rs5215 and rs5219. [GWAS:Type 2 diabetes]
Frequency: 33.0%
References:1
References:1
1.63x increased nephropathy risk among type-1 diabetics
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rs2281999 and rs13293564 (G/T) diabetic nephropathy type-1 diabetes case/control (1176/1323) study from 3 European populations *odds ratio (OR) for DN associated with the TT genotype was 1.68 [95%CI, 1.29 - 2.19], p = 1.0 10(-4)) replicated in an independent population of 412 cases and 614 controls, (combined OR of 1.63 [CI: 1.30 - 2.05], p = 2.3 10(-5))
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[GWAS:Type 1 diabetes]
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[GWAS:Type 1 diabetes]
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Repeatedly associated in genome association studies with type-2 diabetes, type-1 diabetes, multiple sclerosis, and coronary artery disease, according to Risk alleles for multiple sclerosis identified by a genomewide study. An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. [GWAS:Hepatitis C induced liver cirrhosis]
Frequency: 37.2%
References:2
References:2
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[GWAS:Type 1 diabetes]
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[PharmGKB:Non-Curated GWAS Results: A novel susceptibility locus for type 1 diabetes on Chr12q13 identified by a genome-wide association study (Initial Sample Size: 563 cases, 1,146 controls, 483 trios; Replication Sample Size: 549 families, 1092 individuals from 364 trios; Risk Allele: rs1701704-C).] [GWAS:Alopecia areata] [GWAS:Type 1 diabetes]
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[GWAS:Type 1 diabetes]
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[OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 10; CELIAC10]
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rs439121 was identified as a type-1 diabetes risk
1.3x risk
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In an expanded follow-up study of >6,000 controls and 6,000 patients, in which rs2292239 was chosen to replace the nearby rs11171739 originally determined to be associated with type-1 diabetes, the heterozygote odds ratio for this SNP was recalculated to be 1.28 (CI 1.20 - 1.36). [PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample Size: 6,225 cases, 6,946 controls, 3,064 trios); (Region: 12q13.2; Reported Gene(s): ERBB3; Risk Allele: rs2292239-A); (p-value= 0.0000000000000003).This variant is associated with Type 1 diabetes.] [OMIM:V-ERB-B2 AVIAN ERYTHROBLASTIC LEUKEMIA VIRAL ONCOGENE HOMOLOG 3; ERBB3] [GWAS:Type 1 diabetes] [GWAS:Ty...
Frequency: 41.6%
References:2
References:2
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[GWAS:Type 1 diabetes]
1.3x risk of type-1 diabetes
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rs2544677 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.34 (CI 1.00-1.79), and for homozygotes, 1.65 (CI 1.24-2.18).
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample Size: 6,225 cases, 6,946 controls, 3,064 trios); (Region: 16p13.13; Reported Gene(s): C16orf75, PRM3, TNP2; Risk Allele: rs416603-T); (p-value= 0.000003).This variant is associated with Type 1 diabetes.] [GWAS:Type 1 diabetes]
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[OMIM:?] [GWAS:Type 1 diabetes]
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rs1445898 is associated with some protection from type-1 diabetes in several European populations. [GWAS:Type 1 diabetes]
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[PharmGKB:Non-Curated Follow up analysis of genome-wide association data identifies novel loci for type 1 diabetes. (Initial Sample Size: 563 cases, 1,146 controls, 483 case-parents trios; Replication Sample Size: 636 families, 3,303 cases, 4,673 controls); (Region: 6q15; Reported Gene: BACH2; Risk Allele: rs3757247-A) This variant is associated with Type 1 diabetes.] [GWAS:Type 1 diabetes]
Frequency: 45.1%
References:6
References:6
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[GWAS:Type 1 diabetes]
Frequency: 45.1%
References:10
References:10
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[PharmGKB:Non-Curated Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample Size: 6,225 cases, 6,946 controls, 3,064 trios); (Region: 6q15; Reported Gene: BACH2; Risk Allele: rs11755527-G) This variant is associated with Type 1 diabetes.] [OMIM:DIABETES MELLITUS, INSULIN-DEPENDENT; IDDM] [GWAS:Type 1 diabetes]
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[PharmGKB:Non-Curated Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample Size: 6,225 cases, 6,946 controls, 3,064 trios); (Region: 15q25.1; Reported Gene: CTSH; Risk Allele: rs3825932-C) This variant is associated with Type 1 diabetes.] [OMIM:DIABETES MELLITUS, INSULIN-DEPENDENT; IDDM] [GWAS:Type 1 diabetes]
Frequency: 46.0%
Repute:Bad
References:3
Repute:Bad
References:3
1.5x risk of type-1 diabetes
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rs11052552 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.49 (CI 1.28-1.73), and for homozygotes, 1.43 (CI 1.21-1.69). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,963 cases, 2,938 controls; Replication Sample Size: (see Todd 2007); Risk Allele: rs11052552-G). This variant is associated with type 1 diabetes.] [GWAS:Type 1 diabetes]
1.2x increased type-1 diabetes risk; 1.2x increased multiple sclerosis risk
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associated with type-1 diabetes In a separate study, Sardinians with either type-1 diabetes (1,037 patients) or multiple sclerosis (1,498 patients) plus matched controls were genotyped for rs725613. In this study, the rs725613(A) allele was positively associated not only with type-1 diabetes (odds ratio 1.15, p = 5.1 x 10e-3) but also with multiple sclerosis (odds ratio = 1.21, p = 6.7 x 10e-5). rs725613 was strongly associated with T1D in the Han Chinese population (P = 0.00007, odds ratio (OR) = 0.527, 95% confidence interval (CI) = 0.383-0.726) Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes. The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. [OMIM:C-TYPE LECTIN DOMAIN...
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Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Mapping the genetic architecture of gene expression in human liver. [PharmGKB:Curated A genome-wide association study in 2,000 individuals for each of 7 major diseases and a shared set of 3,000 controls found an association of this SNP with type 1 diabetes.] [GWAS:Type 1 diabetes]
1.3x risk of type-1 diabetes
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rs2296336 has been reported in a Swedish study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.3 (CI 1.00-1.69), and for homozygotes, 2.9 (CI 1.88-4.59). suggests this SNP does not play a direct role in type-1 diabetes, and was only seen in the previous study due to being in linkage disequilibrium with specific alleles of the HLA DQB1 gene.
0.6x decreased risk for diabetic nephropathy in females with type-1 diabetes; increased malaria risk
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rs5498, also known as E469K or K469E, is a SNP in the ICAM1 gene that has been associated in some studies (and not others) with risk for type-1 diabetes (T1D). Studies involving Swedish and Japanese T1D patients have reported one or the other of the rs5498 alleles to represent increased T1D risk; studies involving British, Finnish, and Danish patients have not seen any association between rs5498 and T1D . In a study of the type-1 diabetes complication known as diabetic nephropathy (DN), 662 (312 female/350 male) T1D patients with DN and 620 (369/251) without DN were studied (all were Swedish Caucasians). The rs5498(G) allele was found to be significantly associated with decreased risk for diabetic nephropathy specifically in female T1D patients, with an odds ratio of 0.692 (CI: 0.5-0.958, ...
Frequency: 46.9%
Repute:Bad
References:28
Repute:Bad
References:28
1.6x risk of type-1 diabetes
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rs12708716 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.19 (CI 0.97-1.45), and for homozygotes, 1.55 (CI 1.27-1.89). In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 0.81 (CI 0.77-0.86). Tested in a large multiple sclerosis data set consisting of 2369 trio families, 5737 cases and 10 296 unrelated controls, SNP rs12708716 was associated with disease risk (p = 1.6 x 10e-16) [PharmGKB:Curated GWAS results: Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample...
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Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Shared and distinct genetic variants in type 1 diabetes and celiac disease. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 9; CELIAC9] [GWAS:Celiac disease]
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[PharmGKB:Non-Curated Follow up analysis of genome-wide association data identifies novel loci for type 1 diabetes. (Initial Sample Size: 563 cases, 1,146 controls, 483 case-parents trios; Replication Sample Size: 636 families, 3,303 cases, 4,673 controls); (Region: 15q14; Reported Gene: RASGRP1; Risk Allele: rs8035957-C) This variant is associated with Type 1 diabetes.] [GWAS:Type 1 diabetes]
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rs2292399 and rs2903692 both significantly associated with type 1 diabetes odds ratio 1.37 and 1.28. A joint analysis revealed that rs3087243, rs2292399, and rs2903692, but not INS rs689, were significant risk factors for the cooccurrence of AITD [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene (Initial Sample Size: 561 cases, 1,143 controls, 467 trios; Replication Sample Size: 1,333 individuals in 549 families; 390 trios; Risk Allele: rs2903692-G).] [OMIM:C-TYPE LECTIN DOMAIN FAMILY 16, MEMBER A; CLEC16A] [GWAS:Type 1 diabetes]
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[GWAS:Type 1 diabetes]
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A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Novel association in chromosome 4q27 region with rheumatoid arthritis and confirmation of type 1 diabetes point to a general risk locus for autoimmune diseases. Only one independent genetic association with rheumatoid arthritis within the KIAA1109-TENR-IL2-IL21 locus in Caucasian sample sets: confirmation of association of rs6822844 with rheumatoid arthritis at a genome-wide level of significance. [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 6; CELIAC6] [GWAS:Type 1 diabetes]
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[GWAS:Type 1 diabetes]
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Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. Investigation of type 1 diabetes and coeliac disease susceptibility loci for association with juvenile idiopathic arthritis. [PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs1464510-A).] [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 11; CELIAC11] [GWAS:Celiac disease] [GWAS:Celiac disease]
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rs2259571 shows association with type-1 diabetes in Norwegian families, and is independent of the DRB1-DQA1-DQB1 genes
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This SNP is unclear. According to GWAS one study says risk allele is A, another study says risk allele is C. Ambiguous flip ? Abstract associated with type-1 diabetes, organ-specific autoimmune diseases, including Graves' disease. (odds ratio 1.47 (CI: 1.23–1.76, p = 1.9 x 10<sup>–5</sup>) This polymorphism may also contribute to several other autoimmune disorders. A study of 261 Chinese patients with Graves' disease failed to find any association with rs1990760. A study of 591 French Caucasian multiple sclerosis trio families found no association between rs1990760 or rs2068330 and the disease, which did not confirm one previously reported study. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the...
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Risk alleles for multiple sclerosis identified by a genomewide study. Two-stage joint selection method to identify candidate markers from genome-wide association studies. [GWAS:Type 1 diabetes]
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[GWAS:Type 1 diabetes]
Frequency: 54.1%
References:9
References:9
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associated with type-1 diabetes
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[GWAS:Type 1 diabetes]
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[GWAS:Type 1 diabetes]
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[GWAS:Type 1 diabetes]
Frequency: 59.5%
Repute:Bad
References:11
Repute:Bad
References:11
slightly increased risk for several autoimmune diseases
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rs12150220 is a SNP in the NLRP1 gene, which encodes the NACHT leucine-rich-repeat protein 1. SNPs in this gene may be involved in higher risk for several autoimmune diseases. In a study investigating large patient cohorts from six different autoimmune diseases, including autoimmune Addison's disease (n=333 patients), type-1 diabetes (n=1086), multiple sclerosis (n=502), rheumatoid arthritis (n=945), systemic lupus erythematosus (n=156) and juvenile idiopathic arthritis (n=505), plus 3273 healthy controls, the rs12150220(A) allele was associated with higher risk for both autoimmune Addison's disease (odds ratio 1.25, CI: 1.06-1.49, p = 0.007) and type-1 diabetes (odds ratio 1.15, CI: 1.04-1.27, p = 0.005). [OMIM:NLR FAMILY, PYRIN DOMAIN-CONTAINING 1; NLRP1]
normal risk of rheumatoid arthritis, SLE, Sjögren's syndrome, type-1 diabetes, and primary biliary cirrhosis.
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune dise...
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[GWAS:Type 1 diabetes]
1.1x increased risk for schizophrenia
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rs6932590 is a SNP that is postulated to have a role in conferring increased susceptibility for schizophrenia. rs6932590 lies in the major histocompatibility complex (MHC) region on chromosome 6, a region that codes for several genes with significant roles in autoimmunity, such as human leukocyte antigens. Specifically, rs6932590 lies in an intergenic region between PRSS16 (a serine protease expressed in the thymus that plays a role in positive T cell selection) and POM121L2 (a membrane glycoprotein) . The T allele at rs6932590 purportedly confers an increased risk for schizophrenia, with reported odds ratios of 1.16 and 1.31 . === Evidence === One large-scale case-controlled genome-wide association study (GWAS) that examined differential genotypes in individuals with schizophrenia, found ...
Frequency: 68.1%
Repute:Bad
References:10
Repute:Bad
References:10
a slight increase in risk of developing multiple sclerosis
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The (G) allele of rs12722489, located in the first intron of the IL2RA gene, is associated with a slight increase (25%) in risk of developing multiple sclerosis. [PMID tbd; NEJM 357, 29 July 2007, DA Hafler et al.] Note that the (G) allele is the most common at this position in all known populations. blog post giving perspective on the significance of this snp plos rs12722489 and rs2104286 influence multiple sclerosis and type-1 diabetes Haplotypic analysis of Wellcome Trust Case Control Consortium data. IL2RA and IL7RA genes confer susceptibility for multiple sclerosis in two independent European populations. The complex genetics of multiple sclerosis: pitfalls and prospects. Refining genetic associations in multiple sclerosis. IL2RA genetic heterogeneity in multiple sclerosis and type 1 ...
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[GWAS:Type 1 diabetes]
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[PharmGKB:Non-Curated Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample Size: 6,225 cases, 6,946 controls, 3,064 trios); (Region: 10p15.1; Reported Gene: PRKCQ; Risk Allele: rs947474-G) This variant is associated with Type 1 diabetes.] [OMIM:DIABETES MELLITUS, INSULIN-DEPENDENT; IDDM] [GWAS:Type 1 diabetes]
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linked to Crohn's disease and type-1 diabetes Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants. Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1). The expanding genetic overlap between multiple sclerosis and type I diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1. Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cyto...
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rs7202877 is located at chromosome 16q23.1. in the intergenic region ~6 Kb upstream of CTBR2 and CTBR1, and ~54 Kb from BCAR1. This SNP has been associated with increased risk for type-1 diabetes and type-2 diabetes . Diabetes is a disease that affects how the body metabolizes glucose, and is characterized by high levels of glucose in the blood. Overtime, this can cause serious health problems in the eyes, kidneys, heart, nerves and teeth. Meanwhile, insulin is a hormone that helps the cells to uptake glucose for energy. There are two types of diabetes: type 1 and type 2. In type 1 diabetes, the pancreas does not produce insulin. The main factors contributing to the development of this type of diabetes are genetics and exposure to certain viruses . In type 2 diabetes, the pancreas does not...
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[GWAS:Type 1 diabetes]
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rs11594656 increases susceptibility to Type I Diabetes 1.19 times for heterozygotes (AT) and 1.38 times for homozygotes (TT) [OMIM:INTERLEUKIN 2 RECEPTOR, ALPHA; IL2RA]
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[GWAS:Type 1 diabetes]
1.1x risk for type-1 diabetes
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rs17166496 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 0.77 (CI 0.68-0.87), and for homozygotes, 1.09 (CI 0.92-1.29). Note: orientation of SNP is presumed correct but should be confirmed
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[PharmGKB:Non-Curated Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample Size: 6,225 cases, 6,946 controls, 3,064 trios); (Region: 2p23.3; Reported Gene: Intergenic; Risk Allele: rs2165738-C) This variant is associated with Type 1 diabetes.] [GWAS:Type 1 diabetes]
normal
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rs9272346 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 5.49 (CI 4.83-6.24), and for homozygotes, 18.52 (CI 12.69-27.03). Note that the (A) allele is the most common in various human populations; instead of labeling (A) as a risk allele, we could consider the (G) allele protective. Risk alleles for multiple sclerosis identified by a genomewide study. Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. [PharmGKB:Curated GWAS ...
common in clinvar
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suggested the contribution of rs237025 to type-1 diabetes, however in this failed to replicate. This SNP is also known as Met55Val, M55V, or A163G. This was the first SNP in SNPedia. The type 1 diabetes susceptibility gene SUMO4 at IDDM5 is not associated with susceptibility to rheumatoid arthritis or juvenile idiopathic arthritis. Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. Evidence for the role of small ubiquitin-like modifier 4 as a general autoimmunity locus in the Japanese population. SUMO4 M55V variant is associated with diabetic nephropathy in type 2 diabetes. Association study of NFKB1 and SUMO4 polymorphisms in Chinese patients with pso...
normal
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rs213950, a SNP in the cystic fibrosis CFTR gene (but not one that is linked to cystic fibrosis), has been reported in a large study to be associated with type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.09 (CI 1.04–1.15). [OMIM:CFTR POLYMORPHISM]
Magnitude: 0
Frequency: 40.7%
References:16
Frequency: 40.7%
References:16
normal
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rs17388568 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.26 (CI 1.11-1.42), and for homozygotes, 1.58 (CI 1.27-1.95). In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.11 (CI 1.05–1.18). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,963 cases, 2,938 controls; Replication Sample Size: (see Todd 2007); Risk Allele: rs17388568-A). This variant is associated with type 1 diabetes.] [OMIM:DIABETES MELLITUS, INSULIN-DEPENDENT; IDDM] [GWAS:None] [GWAS:...
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rs3118470 increases susceptibility to Type I Diabetes 1.28 times for carriers of the C allele Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1). Joint genetic susceptibility to type 1 diabetes and autoimmune thyroiditis: from epidemiology to mechanisms. Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes. Genetic association between the interleukin-2 receptor-alpha gene and mode of onset of type 1 diabetes in the Japanese population. Overview of the Rapid Response data. Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families. [GWAS:Alopecia areata]
normal
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rs2639703 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.15 (CI 1.02-1.31), and for homozygotes, 1.61 (CI 1.31-1.99).
1.7x risk for RA; 1.6X for T1D; also MS?
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rs2104286 has also been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.30 (CI 1.02-1.65), and for homozygotes, 1.57 (CI 1.25-1.99). The same (A) allele of rs2104286, which is located in the first intron of the IL2RA gene, was calculated to confer a slight increase (19%) in the risk of developing multiple sclerosis. [PMID tbd; NEJM 357, 29 July 2007, DA Hafler et al.] Note that the (A) allele is the most common at this position in all known populations. blog post giving perspective on the significance of this SNP with respect to multiple sclerosis news announcement rs2104286 was significantly associated with UK cases of juvenile idiopathic arthritis (JIA)(allelic odds ra...
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Newly identified genetic risk variants for celiac disease related to the immune response. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. Shared and distinct genetic variants in type 1 diabetes and celiac disease. Association study of the IL18RAP locus in three European populations with coeliac disease. Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associatio...
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[PharmGKB:Non-Curated Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. (Initial Sample Size: 1,167 cases, 777 controls; Replication Sample Size: 1,855 cases, 3,091 controls); (Region: 1q32.1; Reported Gene: IL10; Risk Allele: rs3024505-T) This variant is associated with Ulcerative colitis.] [OMIM:INFLAMMATORY BOWEL DISEASE 23; IBD23] [GWAS:Ulcerative colitis]
common in complete genomics
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People with the human leukocyte antigen (HLA) genotype DRB1*0301-DQA1*0501-DQB1*0201/DRB1*04-DQA1*0301-DQB1*0302 (more simply known as 'DR3/4-DQ8') are at the highest risk of developing type-1 diabetes. The rs2040410(A) allele is associated with DRB1*0301, and the rs7454108(C) allele is associated with DQB1*0302 (and thus DQ8). Instead of more traditional antibody-based tests, two SNPs (rs2040410 and rs7454108) can be used to identify the presence or absence of the DR3/4-DQ8 genotype and thus the highest-risk heterozygous genotype associated with type-1 diabetes. For users of Promethease, this is determined via Gs121.
common on affy axiom data
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HLA-DQB1 8.1 haplotype is associated with significantly lower risk for type-1 diabetes *rs2157678(T) *rs3130380(A) *rs3094628(C) *rs3130352(T)
common on affy axiom data
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association with rheumatoid arthritis and type-1 diabetes point to a general risk locus for autoimmune diseases. Also, of SNPs outside the HLA region, this SNP and one other (rs13119723) in the region of the IL21 gene showed the strongest association with celiac disease in a study of ~800 Caucasian patients and a meta-analysis of two further populations. A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci. Association study of IL2/IL21 and FcgRIIa: significant association with the IL2/IL21 region in Scandinavian coeliac disease families. Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Gene variants influencing mea...
common on affy axiom data
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[PharmGKB:Non-Curated Follow up analysis of genome-wide association data identifies novel loci for type 1 diabetes. (Initial Sample Size: 563 cases, 1,146 controls, 483 case-parents trios; Replication Sample Size: 636 families, 3,303 cases, 4,673 controls); (Region: 1p22.3; Reported Gene: EDG7; Risk Allele: rs1983853-?) This variant is associated with Type 1 diabetes.] [GWAS:Type 1 diabetes]
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
normal
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rs6679677 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.98 (CI 1.72-2.27), and for homozygotes, 3.32 (CI 1.93-5.69). rs6679677 was also reported in the same study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.82 (CI 1.59-2.09), and for homozygotes, 5.19 (CI 3.15-8.55). Recently (Feb 2008), it has been asserted that the association between rs6679677 and type-1 diabetes is actually completely due to a closely linked, potentially causal variant identified as rs2476601, which is also known as Arg620Trp. In this study, apparently the largest to date, the odds ratio...
common on affy axiom data
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HLA-DQB1 8.1 haplotype is associated with significantly lower risk for type-1 diabetes *rs2157678(T) *rs3130380(A) *rs3094628(C) *rs3130352(T)
common on affy axiom data
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HLA-DQB1 8.1 haplotype is associated with significantly lower risk for type-1 diabetes *rs2157678(T) *rs3130380(A) *rs3094628(C) *rs3130352(T)
normal
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rs2542151 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.3 (CI 1.14-1.48), and for homozygotes, 2.01 (CI 1.46-2.76). rs2542151 has been reported in the same study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.30 (CI 1.15-1.47), and for homozygotes, 1.62 (CI 1.17-2.24). In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.30 (CI 1.22–1.40). [PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide association study data identifies additional type 1 diabete...
common in clinvar
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Compared with individuals without CCR5-Delta32 (a variation in another gene) or rs1799864(A), individuals with one or two copies of rs1799864(A) had a 58% lower risk of developing AIDS during the first 4 years after testing positive for HIV, a 19% lower risk during the subsequent 4 years, and no significant protection thereafter. No protective effect (ie no benefit) was seen for this SNP once AIDS had developed. rs1799864(G), rs3025058(A) and rs662 were associated with increased risk, and rs1800775(A) with reduced risk of recurrent venous thromboembolism [OMIM:HUMAN IMMUNODEFICIENCY VIRUS TYPE 1, RESISTANCE TO]
Magnitude: 0
Frequency: 81.4%
Repute:Good
References:4
Frequency: 81.4%
Repute:Good
References:4
common in complete genomics
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Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Contrasting genetic association of IL2RA with SLE and ANCA-associated vasculitis. Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions. Overview of the Rapid Response data. Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families. [PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. (Initial Sample Size: 3,561 cases, 4,646 controls; Replication Sample Size: 6,225 cases, 6,946 controls, 3,064 trios); (Region: 10p15.1; Reported Gene(s): IL2RA; Risk Allele: rs12251307-T); (p-value= 0.0000...
Magnitude: 0
Frequency: 81.5%
Repute:Good
References:14
Frequency: 81.5%
Repute:Good
References:14
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs17810546-G).] [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 10; CELIAC10] [GWAS:Celiac disease] [GWAS:Celiac disease]
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:26
Frequency: 85.8%
Repute:Good
References:26
common in complete genomics
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One report based on a study of 480 Danish families indicated that the rs3772534 SNP in the CBLB gene indicated an increased risk for developing type 1 diabetes, and that there might be co-inheritance with the rs3087243 SNP found in the CTLA4 gene. However, a subsequent study based on over 2,000 parent-child trios (ie families) failed to find any evidence of either effect.
Magnitude: 0
Frequency: 96.9%
Repute:Bad
References:0
Frequency: 96.9%
Repute:Bad
References:0
>1.3x risk
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rs12094543, a SNP in the ZMYM4 gene, has been reported in a large study to be associated with type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.27 (CI 1.05–1.55). Note: the risk allele is believed to be (G), but should be confirmed.
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
common in complete genomics
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rs35667974, also known as Ile923Val, is a SNP in the interferon induced with helicase C domain 1 IFIH1 gene. A recent study apparently found this SNP had the strongest association with type-1 diabetes; however, in a study of 3,000 European multiple sclerosis patients, no association was seen. [PharmGKB:Curated Rare variants (Minor allele frequency less than 3%) in candidate genes were identified by resequencing of exons and splice sites in pools of cases and controls. These were then tested in 8379 cases and 10,575 controls (from Great Britain) and in 3165 families from Europe and the USA, and the minor allele G of rs35667974 was found to be associated with a protective effect(case-control: 95% CI OR = 0.51; families: 95% CI RR = 0.60) against Diabetes Mellitus, Insulin-Dependent (combine...
Magnitude: 0
Repute:Good
References:17
Repute:Good
References:17
common in complete genomics
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rs41295061 increases susceptibility to Type I Diabetes 1.67 times for heterozygotes (AC) and 2.27 times for homozygotes (CC)
normal
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rs5219, also known as E23K, is a SNP in the KCNJ11 gene. The association between type-1 diabetes and rs5219 is mentioned as being replicated in ; there is also a 90% correlation between rs5219 and rs5215. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under an additive model, the odds ratio for the minor (risk) allele (T) is 1.15 (CI: 0.95-1.4, p=0.2, ie not significant). But for the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). Genotyping of ~4000 Chinese as well a meta-analysis concluded that rs5219 was associated with type-2 diabet...
common on affy axiom data
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HLA-DQB1 8.1 haplotype is associated with significantly lower risk for type-1 diabetes *rs2157678(T) *rs3130380(A) *rs3094628(C) *rs3130352(T)
116 snps
(hide) Type-2 diabetes
Magnitude: 2.5
Frequency: 38.9%
Repute:Bad
References:118
Frequency: 38.9%
Repute:Bad
References:118
increased risk for type-2 diabetes
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rs13266634 is a SNP in the zinc transporter protein member 8 SLC30A8 gene that has primarily been associated with type-2 diabetes in several studies. This SNP is also known as the Arg325Trp or R325W variant; the (C) allele encodes the arginine (R), and the (T) allele encodes the tryptophan (W). significantly associated p = 0.0073; in 1,630 Japanese subjects with type-2 diabetes and in 1,064 controls The major alleles of the SLC30A8 SNP rs13266634 and the HHEX SNP rs7923837 associate with reduced insulin secretion, but not with insulin resistance. 46% of European non-diabetic offspring of type-2 diabetes patients are rs13266634(C;C) homozygotes; they are diabetes-prone and characterised by a 19% decrease in first-phase insulin release following an intravenous glucose load. * Note: this SNP,...
1.2x increased risk for type-2 diabetes
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rs4402960 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.23 (CI: 1.11-1.36, p = 8.1 x 10e-5) associated with type-2 diabetes significantly associated with type-2 diabetes p = 0.00009; in 1,630 Japanese subjects and in 1,064 controls 1,638 type-2 diabetes patients and 1,858 controls *rs4402960 borderline (OR 1.10, 95% CI: 0.99-1.22). Neither rs4402960 or rs1470579 were found to be associated with type-2 diabetes in a study of 3,000 French Caucasians. This SNP was confirmed to be associated with type-2 diabetes in a study of 500+ Japanese patients plus pooled meta-analysis with 6 previous association studies (also of Japanese). Note: rs4402960 is fairly tightly linked (r<sup>2</sup>=0.87) with another IGF2BP2 gene SNP also asso...
1.38x increased risk for prostate cancer
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rs4430796 is a SNP in the TCF2 gene on chromosome 17q12, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs4430796 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On its own, the rs4430796(A;A) risk genotype - in dbSNP orientation, not as published - yields an odds ratio for developing prostate cancer of 1.38 (CI: 1.21-1.57, p=1.6x10e-6) and may account for 10.2% of population attributable risk. article linking to Prostate cancer and type-2 diabetes 403 non-Hispanic white families were studied, totaling 1,015 men, to reach the conclusion that the rs4430796(A) allele is associated with increased prostate cancer risk; the odds ratio was 1.40 (CI: 1.09-1.81) ...
Avg. fasting Plasma Glucose 5.18 mmol/L (93 mg/dl). Slightly higher blood glucose. Fasting Plasma Glucose is the amount of sugar in your blood when you wake up. It's required to power your body, but too much is very bad for you. Fasting plasma glucose between 5.6 mmol/L and 6.9 mmol/L (101 – 125 mg/dl) is considered pre-diabetes. Fasting plasma glucose higher than 7 mmol/L (126 mg/dl) is considered diabetes.
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rs560887, p = 4 x 10(-7)) *654 normoglycemic subjects, replicated in 9,353 subjects *fasting plasma glucose (FPG) (beta = -0.06 mmol/l per A-allele, combined p = 4 x 10(-23)) and with pancreatic beta-cell function (Homa-B model, combined p = 3 x 10(-13)) in three populations; however it was not associated with type 2 diabetes risk. (ageing) Blood Glucose [PharmGKB:Non-Curated Phenotype 1: In a meta-analysis of 21 GWAS cohorts followed by analysis in additional individuals, this SNP was found to be associated with fasting glucose level. Study size: 119,169. Significance metric(s): p = 8.7 x 10(-218). Phenotype 2: In the same study, this SNP was found to be associated with HOMA-B (homeostasis model assessment of beta-cell function). Study size: 94,839. Significance metric(s): p = 1.5 x 10(-...
1.3x increased risk for Type 2 Diabetes. Mothers have babies 27g heavier. Slightly increased Birth Weight for babies whose mother has this SNP.
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rs1799884, known also as the -30 SNP of the GCK gene, has been associated with type-2 diabetes. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under a recessive model, the odds ratio for rs1799884(A;A) homozygotes is 2.70 (CI: 1.51-4.83, p=0.0008); under an additive model, the odds ratio is 1.34 (CI: 1.07-1.69, p=0.01). For the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). A common haplotype of the glucokinase gene alters fasting glucose and birth weight: association in six studies and population-genetics analyses. Type 2 diabetes TCF...
Magnitude: 2
Frequency: 29.2%
Repute:Bad
References:107
Frequency: 29.2%
Repute:Bad
References:107
1.2x increased risk for type-2 diabetes
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rs10811661 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.27 (CI: 1.15-1.40, p = 1.9 x 10e-6) rs10811661 is mentioned in part 2 of a series significantly associated with type-2 diabetes p = 0.0024; in 1,630 Japanese subjects with type-2 diabetes and in 1,064 controls 1,638 type 2 diabetes patients and 1,858 controls *rs10811661 in the vicinity of CDKN2B (OR 1.20, 95% CI: 1.06-1.37, p = 0.004) T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for *CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) *CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) *IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, in...
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
Magnitude: 2
Frequency: 30.1%
Repute:Bad
References:106
Frequency: 30.1%
Repute:Bad
References:106
1.3x increased type-2 diabetes risk
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This SNP is in the TCF7L2 gene, and has been linked to type-2 diabetes, breast cancer and aggressive prostate cancer. This SNP is also known as IVS4G>T. is the paper which links it to Breast cancer. It suggests the T allele as increasing risk. reports the association of rs12255372 and rs7903146 with Type-2 diabetes in a Finnish sample. rs12255372 Common variants (rs12255372 and rs7903146) in TCF7L2 seem to be associated with an increased risk of diabetes among persons with impaired glucose tolerance Considered for type-2 diabetes with rs7903146 rs12255372 rs10885406. Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion as measured by acute insulin response and adjusted for the degree of insulin sensitivity (p = 0.036). In a study of 1,457 prostate cancer case...
3.2x risk for T2D
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rs7923837 is a SNP of the HHEX homeobox gene. In several studies, it has been associated with risk for type-2 diabetes (T2D). In a study of 500 unrelated Caucasian T2D patients, the rs7923837(G) allele was overrepresented; the odds ratio was 1.57 (CI: 1.08-2.27, p=0.017). In this population, the population attributable risk for this allele was estimated to be 33%. In a study of ~400 Japanese T2D patients, rs7923837(G) was also associated with type-2 diabetes (odds ratio 1.66, CI: 1.28-2.15, p=0.00014). Heterozygous and homozygous carriers of the risk allele had odds ratios of 1.57 (95% CI 1.15-2.16, p=0.0050) and 3.16 (95% CI 1.40-7.16, p=0.0038) relative to non-carriers. rs7923837 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.27 (CI: 1...
Normal (lower) risk of Type 2 Diabetes and Gestational Diabetes. Normal insulin secretion in the pancreas. This has been confirmed in most races.
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This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). This SNP is also known as IVS3C>T. rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. Full text of the paper is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse population Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion...
1.78x increased risk of developing Type-2 diabetes
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rs358806 has been reported in a large study to be associated with type-2 diabetes. The risk allele is (C); the odds ratio associated with heterozygotes is 0.86 (CI 0.75-0.97), and for homozygotes, 1.78 (CI 1.34-2.36). [PharmGKB:Non-Curated GWAS results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,924 cases, 2,938 controls; Replication Sample Size: (see Zeggini 2007)). This variant is associated with Type 2 diabetes.] [GWAS:Type 2 diabetes]
less IL6; certain risks, see details rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. The (C;C) genotype is found almost exclusively in the caucasian populations. It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. The [rs1800795(C) allele, generally associated with lower levels of IL6, has been associated with increased risk in these studies: * rs1800795 (C;C) and (C;G) Caucasians who are excessively heavy (body mass index ~33 +/- 5kg/m2) are at increased risk (odd...
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
1.9x increased risk for type-2 diabetes
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rs4506565 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.36 (CI 1.2-1.54), and for homozygotes, 1.88 (CI 1.56-2.27). Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs7903146. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. [PharmGKB:Curated Phenotype: In a meta-analysis of 21 GWAS cohorts, this SNP was found to be associated with fasting glucose level. Study size: 46,181. Significance metric(s): p = 1.2 x 10(-8). Study population/ethnicity: Non-diabetic Individuals of European descent....
lower risk of obesity and Type-2 diabetes
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rs9939609 is a SNP in the fat mass and obesity associated FTO gene, aka the 'Fat Gene' The original paper describing it is here . [http://www.alzforum.org/new/detail.asp?id=1567 The researchers identified 10 different FTO SNPs in the first intron of the gene that associated with both BMI and type-2 diabetes. Because they all correlated with each other, they chose to examine one of the SNPs (rs9939609) in detail. rs9939609 has also been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.34 (CI 1.17-1.52), and for homozygotes, 1.55 (CI 1.3-1.84). In a different study, this SNP was found in a linkage block in the FTO gene with rs1121980; see rs1121980 for the association of th...
1.32x increased risk of early-onset type-2 diabetes
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rs2295490 is a SNP in the tribbles homolog 3 TRIB3 gene, also known as Q84R. The (A) allele encodes the Gln (Q), while the (G) allele encodes the Arg (R). A study involving four different case-control samples comprising a total of 5469 Caucasisans determined that rs2295490(G) was nominally associated with type-2 diabetes (odds ratio 1.17, CI: 1.00-1.36, p = 0.04). When stratified by age of diabetes onset, these carriers had an increased risk of early-onset T2D (OR 1.32, CI: 1.10-1.58, p = 0.002). this gain of function mutation may affect insulin signaling and increase the risk of insulin resistance [PharmGKB:Curated This variant in the TRIB3 gene is associated with early-onset T2D in Whites. This Q84R %22gain of function%22 polymorphism, impairs insulin signaling.]
slightly higher risk of developing Parkinson's Disease for caucasians but it has failed to reproduce in Greeks and Chinese populations. If there is an effect is is very small.
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People with two copies of the T allele at rs6812193 appear to have a slightly lower risk of Parkinson's disease. The same researchers identified another risk allele for Parkinson's disease at rs11868035. plos [GWAS:Parkinson's disease]
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[GWAS:None]
1.2x increased risk for type-2 diabetes
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rs1470579 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.18 (CI: 1.07-1.31, p = 8.3 x 10e-4) T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for *CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) *CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) *IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24) Neither rs4402960 or rs1470579 were found to be associated with type-2 diabetes in a study of 3,000 French Caucasi...
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[PharmGKB:Non-Curated GWAS results: SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. (Initial Sample Size: 194 Japanese cases, 1,558 Japanese controls; Replication Sample Size: 4,924 cases, 2,618 controls (Japanese), 1433 cases, 1,735 controls (Singaporean), 3,891 cases, 4,888 controls (Danish)); (Region: 3q27.2; Reported Gene(s): IGF2BP2; Risk Allele: rs6769511-C); (p-value= 0.000000001).This variant is associated with Type 2 diabetes.] [GWAS:Type 2 diabetes]
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4.9x risk of type-2 diabetes among women carriers of both the rare alleles at rs3750425 and rs2274924 when their magnesium intake was lower than 250 mg per day.
Frequency: 16.8%
References:31
References:31
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In a study conducted on 6,580 Nondiabetic Finnish Men, rs10923931 in NOTCH2 gene showed nominal or significant associations with several lipoprotein traits. [GWAS:Type 2 diabetes]
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[GWAS:Type 2 diabetes]
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association with type-2 diabetes
Frequency: 19.5%
References:4
References:4
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[GWAS:None]
1.5x risk
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rs6718526 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.49 (CI 1.05-2.11), and for homozygotes, 1.86 (CI 1.32-2.63).
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[GWAS:Type 2 diabetes]
1.2x risk type-2 diabetes
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rs9465871 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.18 (CI 1.04-1.34), and for homozygotes, 2.17 (CI 1.6-2.95). When combined, each additional risk allele from rs9465871, rs10811661, rs4402960, and rs13266634 increased the risk for type 2 diabetes by 1.24-fold (P = 2.85 x 10(-7)) or for combined IFG/type 2 diabetes by 1.21-fold (P = 6.31 x 10(-11)) in Chinese Hans Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. PPARG, KCNJ11, CDKAL1, CDKN2A-CDKN2B, IDE-KIF11-HHEX, IGF2BP2 and SLC30A8 are associated with type 2 diabetes in a Chinese population. Simultaneous genotype calling and haplotype phasing improves genotype acc...
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In 'Association of the ADRA2A polymorphisms with the risk of type 2 diabetes: a meta-analysis.' a meta-analysis of publications prior to September 2012 showed no overall association between rs553668 and T2D risk, but did find an association with very high (poor) P-value for Europeans under recessive gene model (GT=AA, OR=1.36, p=0.02, 95% CI: 1.05, 1.76). In 'Genetic association of adrenergic receptor alpha 2A with obesity and type 2 diabetes.' rs553668 was found to correlate with obesity in Swedish population, but not significantly for BMI-corrected T2D risk. ADRA2A is involved in sympathetic nervous system's inhibition of insulin secretion and lipolysis, so direct effect on T2D is usually sought, but the Swedish study suggest it could work through body mass. It also mentions that rs55366...
Frequency: 27.4%
Repute:Bad
References:2
Repute:Bad
References:2
2.5x risk
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rs12304921 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 2.50 (CI 1.53-4.09), and for homozygotes, 1.94 (CI 1.20-3.15). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,924 cases, 2,938 controls; Replication Sample Size: (see Zeggini 2007); Risk Allele: rs12304921-G). This variant is associated with type 2 diabetes.] [GWAS:Type 2 diabetes]
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[GWAS:Type 2 diabetes]
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related to Prostate cancer] and Type-2 diabetes The increased risk associated with rs7501939 and the closely linked rs4430796 is approximately doubled in individuals hereditarily predisposed to develop early-onset prostate cancer, based on a study of ~1,000 men. rs7501939 identified as one of three HNF1B gene SNPs associated with decreased risk for prostate cancer in two large prospective studies cancer-genetics these SNPs influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 [OMIM:PROSTATE CANCER, HEREDITARY, 11; HPC11] [GWAS:Prostate cancer]
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[GWAS:Type 2 diabetes]
normal
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rs9326506 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.28 (CI 1.11-1.48), and for homozygotes, 1.46 (CI 1.24-1.72).
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4.9x risk of type-2 diabetes among women carriers of both the rare alleles at rs3750425 and rs2274924 when their magnesium intake was lower than 250 mg per day.
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[GWAS:Type 2 diabetes]
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
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[GWAS:Type 2 diabetes]
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[PharmGKB:Non-Curated GWAS Results: Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes (Initial Sample Size: 4,549 cases, 5,579 controls; Replication Sample Size: 24,194 cases, 55,598 controls; Risk Allele: rs4607103-C).] [GWAS:Type 2 diabetes]
Frequency: 31.9%
References:3
References:3
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[GWAS:Type 2 diabetes]
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[GWAS:None]
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The association between type-1 diabetes and rs5215 is mentioned as being replicated in ; there is also a 90% correlation between rs5215 and rs5219. [GWAS:Type 2 diabetes]
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associated with type-2 diabetes, but then called into question by along with rs9300039 rs4402960 rs7754840 rs17044137 rs11037909 rs1081161 rs1111875 rs7923837 rs12885713 rs1219648 rs2981582 [PharmGKB:Non-Curated GWAS Results: Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes (Initial Sample Size: 1,924 cases, 2,938 controls; Replication Sample Size: 3,757 cases, 5,346 controls; Risk Allele: rs5015480-C).] [GWAS:Type 2 diabetes] [GWAS:Type 2 diabetes]
2.4x risk of [[type-2 diabetes]]
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rs1111875 is a SNP of the HHEX homeobox gene. In several studies, it has been associated with risk for type-2 diabetes (T2D). In a study of 500 unrelated Caucasian T2D patients, the rs1111875(G) allele was overrepresented; the odds ratio was 1.68 (CI: 1.19-2.35, p=0.003). In this population, the population attributable risk for this allele was estimated to be 36%. In a study of ~400 Japanese, rs1111875(G) was also associated with type-2 diabetes (odds ratio 1.42, CI: 1.13-1.78, p=0.0024). Heterozygous and homozygous carriers of the risk allele had odds ratios of 1.31 (CI: 0.97-1.77, p=0.0810) and 2.40 (CI: 1.34-4.32, p=0.0028) relative to non-carriers. And in a third study, 1,630 Japanese patients were also found to have this SNP significantly overrepresented (p=0.0064). rs1111875 replicat...
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part 2 in the series mentions rs564398 Heterogeneity in meta-analyses of genome-wide association investigations. Strong association of common variants in the CDKN2A/CDKN2B region with type 2 diabetes in French Europids. Association analysis of type 2 diabetes Loci in type 1 diabetes. Association analysis in african americans of European-derived type 2 diabetes single nucleotide polymorphisms from whole-genome association studies. Post genome-wide association studies of novel genes associated with type 2 diabetes show gene-gene interaction and high predictive value. Implication of genetic variants near TCF7L2, SLC30A8, HHEX, CDKAL1, CDKN2A/B, IGF2BP2, and FTO in type 2 diabetes and obesity in 6,719 Asians. Worldwide population differentiation at disease-associated SNPs. Assessing the combi...
Frequency: 34.5%
References:1
References:1
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[GWAS:Type 2 diabetes]
Frequency: 35.4%
References:4
References:4
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rs17044137 increases susceptibility to Type II Diabetes 1.13 times for carriers of the A allele [PharmGKB:Curated rs17044137 demonstrated association with Type 2 Diabetes in a GWAS of Finnish and Swedish patients and controls.]
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rs2863389, rs7935082 and rs952635 implicated in type-2 diabetes by
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Associated with type-2 diabetes in a Mexican-American population.
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Repeatedly associated in genome association studies with type-2 diabetes, type-1 diabetes, multiple sclerosis, and coronary artery disease, according to Risk alleles for multiple sclerosis identified by a genomewide study. An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. [GWAS:Hepatitis C induced liver cirrhosis]
Frequency: 37.2%
References:1
References:1
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[GWAS:Type 2 diabetes]
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[GWAS:Type 2 diabetes]
1.5x risk
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rs2930291 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (C); the odds ratio associated with heterozygotes is 1.25 (CI 1.04-1.51), and for homozygotes, 1.50 (CI 1.24-1.82).
Frequency: 38.1%
References:1
References:1
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[GWAS:Type 2 diabetes]
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[GWAS:Type 2 diabetes]
1.3x increased risk for type-2 diabetes
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Polycystic Kidney disease rs7756992 significantly p = 0.0363 associated with type-2 diabetes in 1,630 Japanese subjects and in 1,064 controls rs7756992 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.27 (CI: 1.15-1.40, p = 9.8 x 10e-7) 1,638 type 2 diabetes patients and 1,858 controls *rs7756992 non-significant T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for *CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) *CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) *IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined...
1.18x risk 1.18x risk of type-2 diabetes
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rs2903265 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.18 (CI 0.93-1.49), and for homozygotes, 1.47 (CI 1.17-1.86).
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rs734312, or '''His611Arg''', is a SNP located in exon 8 of the WFS1 gene. An A at this SNP encodes for histamine and a G encodes for arginine. A single study found this SNP to be associated with medication overuse headache (sample consisting of 82 MOH patients). Compared to the His/His genotypes, those carrying two Arg alleles had a significantly higher monthly drug consumption (p = 0.00075) and higher severe depressive scores on the Beck Depression Index (p = 0.003). His611Arg is also potentially implicated in type-2 diabetes. In a sample of 3,234 high diabetes risk individuals, Arg/Arg carriers had a generally higher insulinogenic index and lower insulin sensitivity levels, while His allele carriers followed the opposite pattern. Arg/Arg carriers also responded strongly to metformin and...
1.16x increased risk for type-2 diabetes
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rs3802177 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.16 (CI: 1.05-1.27, p = 4.5 x 10e-3) Note: this SNP is fairly tightly linked (r<sup>2</sup> = 0.83) to another SNP in the SLC30A8 gene also linked to type-2 diabetes, rs13266634 [GWAS:Type 2 diabetes]
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[GWAS:None]
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[GWAS:Type 2 diabetes]
Frequency: 41.0%
References:20
References:20
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obesity and type-2 diabetes *rs1121980 *rs7498665 *rs4752856 *rs17782313 *rs2815752 *rs10938397 The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI. Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants? Common body mass index-associated variants confer risk of extreme obesity. Obesity genotype score and cardiovascular risk in women with type 2 diabetes mellitus. Novel obesity risk loci do not determine distribution of body fat depots: a whole-body MRI/MRS study. From monogenic to polygenic obesity: recent advances. Genetic markers of adult obesity risk are associated with greater early infancy weight gain and growth. Obesity and diabetes genes are ...
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[GWAS:Type 2 diabetes]
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[GWAS:Type 2 diabetes]
Frequency: 42.5%
References:35
References:35
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rs10946398 increases susceptibility to Type II Diabetes 1.14 times for carriers of the C allele [PharmGKB:Non-Curated GWAS results: Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome wide association data. (Initial Sample Size: 1,924 cases, 2,938 controls; Replication Sample Size: 3,757 cases, 5,346 controls); (Region: 6p22.3; Reported Gene(s): CDKAL; Risk Allele: rs10946398-?); (p-value= 0.0000007).This variant is associated with Type 2 diabetes.] [OMIM:CDK5 REGULATORY SUBUNIT-ASSOCIATED PROTEIN 1-LIKE 1; CDKAL1] [GWAS:Type 2 diabetes] [GWAS:Type 2 diabetes]
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associated with type-2 diabetes Association analysis of type 2 diabetes Loci in type 1 diabetes. Metabolic and cardiovascular traits: an abundance of recently identified common genetic variants. Association analysis of variation in/near FTO, CDKAL1, SLC30A8, HHEX, EXT2, IGF2BP2, LOC387761, and CDKN2B with type 2 diabetes and related quantitative traits in Pima Indians. Novel association of HK1 with glycated hemoglobin in a non-diabetic population: a genome-wide evaluation of 14,618 participants in the Women's Genome Health Study. Genetic risk profiling for prediction of type 2 diabetes. [GWAS:Type 2 diabetes]
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Associated with diabetic nephropathy and type-2 diabetes in a Japanese population. [PharmGKB:Non-Curated GWAS results: Genetic variations associated with diabetic nephropathy and type II diabetes in a Japanese population (Initial Sample Size: 94 cases, 94 controls; Replication Sample Size: NR). This variant is associated with Diabetic nephropathy.] [GWAS:Diabetic nephropathy]
Frequency: 42.9%
References:0
References:0
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rs10012946 is in linkage disequilibrium with a polymorphism that increases susceptibility to Type II Diabetes 1.15 times for carriers of the C allele Testing of diabetes-associated WFS1 polymorphisms in the Diabetes Prevention Program. Association analysis of type 2 diabetes Loci in type 1 diabetes. Predicting type 2 diabetes based on polymorphisms from genome-wide association studies: a population-based study. Novel association of HK1 with glycated hemoglobin in a non-diabetic population: a genome-wide evaluation of 14,618 participants in the Women's Genome Health Study. Genome-based prediction of common diseases: methodological considerations for future research. The effect of multiple genetic variants in predicting the risk of type 2 diabetes.
Frequency: 43.4%
References:1
References:1
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[GWAS:Type 2 diabetes]
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Associated with type-2 diabetes in a Mexican-American population.
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Genetic risk profiling for prediction of type 2 diabetes. [GWAS:Type 2 diabetes]
Frequency: 43.4%
References:3
References:3
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rs2863389, rs7935082 and rs952635 implicated in type-2 diabetes by
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obesity and type-2 diabetes *rs1121980 *rs7498665 *rs4752856 *rs17782313 *rs2815752 *rs10938397 Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants? Common body mass index-associated variants confer risk of extreme obesity. Novel obesity risk loci do not determine distribution of body fat depots: a whole-body MRI/MRS study. From monogenic to polygenic obesity: recent advances. A strategy for analyzing gene-nutrient interactions in type 2 diabetes. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study. FTO and MC4R gene variants are associated with obesity in polycystic ovary syndrome. Genetic predictors of weight loss and weig...
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[PharmGKB:Non-Curated GWAS Results: Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes (Initial Sample Size: 4,549 cases, 5,579 controls; Replication Sample Size: 24,194 cases, 55,598 controls; Risk Allele: rs864745-T).] [GWAS:Crohn's disease] [GWAS:Type 2 diabetes]
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Associated with type-2 diabetes in a study of Danish (but apparently not Swedish or French) Caucasians
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The T-allele of NOS1AP rs3020781 was previously reported to be strongly associated with type-2 diabetes in various European-descent populations comprising a total of 2,198 individuals with a combined odds ratio (OR) of 1.53 [1.28-1.81]. However, in a combined study sample comprising a total of 16,801 and 16,913 individuals from Denmark, no significant association was found to diabetes or obesity.
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[PharmGKB:Non-Curated GWAS results: A variant near MTNR1B is associated with increased fasting plasma glucose levels and type 2 diabetes risk. (Initial Sample Size: 2,151 individuals; Replication Sample Size: 6,332 cases, 9,132 controls); (Region: 11q21; Reported Gene(s): MTNR1B; Risk Allele: rs1387153-T); (p-value= 2E-36).This variant is associated with Fasting plasma glucose.] [OMIM:?] [GWAS:Fasting plasma glucose]
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[PharmGKB:Non-Curated GWAS results: Type 2 diabetes whole-genome association study in four populations: the DiaGen consortium. (Initial Sample Size: 500 cases, 497 controls; Replication Sample Size: 2,573 cases, 2,776 controls); (Region: 2q12.1; Reported Gene(s): Intergenic; Risk Allele: rs6712932-?); (p-value= 0.000006).This variant is associated with Type 2 diabetes.] [GWAS:Type 2 diabetes]
Frequency: 46.9%
References:1
References:1
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[GWAS:Type 2 diabetes]
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[GWAS:None]
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[GWAS:Type 2 diabetes]
0.91x decreased risk for T2D
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rs2077119, also known as -469T/G, is a SNP in the alpha-2-HS-glycoprotein AHSG gene. In a study of ~3,800 Danish type-2 diabetes patients, pooled with a previous study, the minor rs2077119(G) allele showed a slight protective effect, with an odds ratio of 0.91 (CI: 0.84-0.99, p=0.007).
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[GWAS:Type 2 diabetes]
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[GWAS:Type 2 diabetes]
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[GWAS:Type 2 diabetes]
Frequency: 50.8%
Repute:Bad
References:60
Repute:Bad
References:60
increased type-2 diabetes risk; higher gestational diabetes risk
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rs10830963 was associated with an increased risk of type-2 diabetes in our Han Chinese cohort (OR 1.16, 95% CI 1.03-1.31, p = 0.015). As previously described, the risk variant was also associated with increased fasting plasma glucose, showing an increase of 0.068 mmol/l (95% CI 0.036-0.100, p = 4 x 10(-5)) per risk allele rs10830962, rs4753426, and rs10830963 were significantly associated with higher fasting plasma glucose concentrations and reduced OGTT- and IVGTT-induced insulin release. rs3781638 displayed significant association with lower fasting plasma glucose levels and increased OGTT-induced insulin release A study totaling 19,000+ Europeans concluded that rs10830963 had the most influence of any MTNR1B gene SNP on the risk for type-2 diabetes. Specifically, the (G) allele increase...
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summary, indicating a small effect of this SNP, seen only in meta-analyses rs3792267 associated with noninsulin-dependent diabetes mellitus, polycystic ovary syndrome, type 2 diabetes, gestational diabetes and obesity [OMIM:CALPAIN 10; CAPN10]
1.4x risk 1.4x risk of type-2 diabetes
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rs7659604 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.35 (CI 1.19-1.54), and for homozygotes, 1.09 (CI 0.91-1.30).
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rs2334499 is in a region of chromosome 11p15 which contains a cluster of imprinted genes. This SNP, rs2334499, has recently been reported to have an association with type-2 diabetes. The allele that confers risk when paternally inherited is protective when maternally inherited. [OMIM:?]
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[GWAS:Type 2 diabetes]
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Associated with type-2 diabetes in a Mexican-American population.
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[OMIM:?] [GWAS:Type 2 diabetes]
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[PharmGKB:Non-Curated GWAS Results: Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes (Initial Sample Size: 4,549 cases, 5,579 controls; Replication Sample Size: 24,194 cases, 55,598 controls; Risk Allele: rs7961581-C).] [GWAS:Type 2 diabetes]
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[GWAS:None]
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rs2721068 was significantly associated with type-2 diabetes
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implicated in type-2 diabetes according to this Gene Sherpas post Extensive blog post theorizing this snp may activate a cryptic exon. Polymorphisms in the transcription factor 7-like 2 (TCF7L2) gene are associated with type 2 diabetes in the Amish: replication and evidence for a role in both insulin secretion and insulin resistance. TCF7L2 polymorphisms are associated with type 2 diabetes in northern Sweden. A genetic variation of the transcription factor 7-like 2 gene is associated with risk of type 2 diabetes in the Japanese population. TCF7L2 gene polymorphisms confer an increased risk for early impairment of glucose metabolism and increased height in obese children. Replication study for the association of TCF7L2 with susceptibility to type 2 diabetes in a Japanese population. Variant...
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rs6698181 increases susceptibility to Type II Diabetes 1.11 times for carriers of the T allele [PharmGKB:Curated rs6698181 demonstrated association with Type 2 Diabetes in a GWAS of Finnish and Swedish patients and controls.]
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rs12197043 and rs4897081 novel associations in type-2 diabetes patients with nephropathy from an African-American population
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rs1053049, rs6902123, and rs2267668 in PPARD affect Lifestyle Intervention induced changes in overall adiposity, hepatic fat storage, and relative muscle mass. Our findings provide a mechanistic explanation for the involvement of these genetic variations in the development of insulin resistance and type-2 diabetes. The myocyte expression of adiponectin receptors and PPARdelta is highly coordinated and reflects lipid metabolism of the human donors.
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[GWAS:Type 2 diabetes]
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rs7294919, showed a particularly strong link to a reduced hippocampus volume, suggesting that this gene is very important to hippocampus development or health. No associations for brain volume, but they did discover that intracranial volume was significantly associated with two loci: rs4273712, a known height locus on chromosome 6q22, and rs9915547, tagging the inversion on chromosome 17q21. *http://www.sciencedaily.com/releases/2012/04/120415151347.htm *http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2237.html *http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2250.html *http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2245.html [GWAS:Type 2 diabetes]
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Novel meta-analysis-derived type 2 diabetes risk loci do not determine prediabetic phenotypes. Genotype score in addition to common risk factors for prediction of type 2 diabetes. Correcting 'winner's curse' in odds ratios from genomewide association findings for major complex human diseases. How many genetic variants remain to be discovered? Utility of genetic and non-genetic risk factors in prediction of type 2 diabetes: Whitehall II prospective cohort study. Type 2 diabetes (T2D) associated polymorphisms regulate expression of adjacent transcripts in transformed lymphocytes, adipose, and muscle from Caucasian and African-American subjects. Genetic risk profiling for prediction of type 2 diabetes. Association between type 2 diabetes genetic susceptibility loci and visceral and subcutaneo...
Frequency: 57.8%
References:0
References:0
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rs12197043 and rs4897081 novel associations in type-2 diabetes patients with nephropathy from an African-American population
Frequency: 60.2%
References:6
References:6
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[GWAS:Type 2 diabetes]
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Genetic risk profiling for prediction of type 2 diabetes. Association study of type 2 diabetes genetic susceptibility variants and risk of pancreatic cancer: an analysis of PanScan-I data. [GWAS:Type 2 diabetes]
Frequency: 65.2%
References:1
References:1
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[GWAS:Type 2 diabetes]
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[GWAS:Type 2 diabetes]
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Type 2 diabetes risk allele near CENTD2 is associated with decreased glucose-stimulated insulin release. Genetic susceptibility to type 2 diabetes and breast cancer risk in women of European and African ancestry. [GWAS:Type 2 diabetes]
Frequency: 69.6%
References:1
References:1
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[GWAS:Type 2 diabetes]
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rs4812829, rs4812829 showed a strong link to an increased susceptibility to type II diabetes in the South Asia population by itself and in Japanese population with five other risk alleles in two different studies [http://www.ncbi.nlm.nih.gov/pubmed/23029454. These results indicate that the genes and/or other factors associated with this SNP are important in the development of type 2 diabetes. rs4812829 is located at 20q13 in the intronic region of HNF4A (Hepatocyte nuclear factor 4 alpha), which encodes a transcription factor that binds DNA as a homodimer HNF4A controls the expression of several genes, including HNF1A (hepatocyte nuclear factor 1 alpha), another transcription factor that regulates hepatic gene expression [http://www.ncbi.nlm.nih.gov/pubmed/23551881 . Mutations in HNF4A hav...
normal
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rs9402571 is a SNP in the serum/glucocorticoid regulated kinase 1 SGK1 gene. Three independent European populations were analyzed, with follow up in 3798 non-diabetic and 659 diabetic (type 2) individuals, for associations between SGK1 SNPs and insulin secretion. In lean non-diabetic individuals, rs9402571(G) minor allele carriers had higher (better) insulin response and lower prevalence of type-2 diabetes, with an odds ratio of 0.85 (CI: 0.7-1.0, p = .065, dominant model).
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[GWAS:Type 2 diabetes]
>1.5x risk for T2D
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rs9300039, a SNP on chromosome 11 that is unusual is being over 1,000,000 base-pairs away from the nearest known gene, has been identified as a risk factor for type-2 diabetes in a study of over 2,000 Caucasian patients. The odds ratio for the risk allele rs9300039(C) was 1.48, (CI: 1.28-1.71, p=5.7x10e-8). This SNP is also mentioned in a related blog series. Called into question by table 1 of Heterogeneity in meta-analyses of genome-wide association investigations. Studies of association of variants near the HHEX, CDKN2A/B, and IGF2BP2 genes with type 2 diabetes and impaired insulin release in 10,705 Danish subjects: validation and extension of genome-wide association studies. Association of CDKAL1, IGF2BP2, CDKN2A/B, HHEX, SLC30A8, and KCNJ11 with susceptibility to type 2 diabetes in a J...
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[GWAS:Type 2 diabetes]
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[PharmGKB:Non-Curated GWAS Results: Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes (Initial Sample Size: 4,549 cases, 5,579 controls; Replication Sample Size: 24,194 cases, 55,598 controls; Risk Allele: rs7578597-T).] [GWAS:Type 2 diabetes]
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rs2268388(T) confers 1.6x odds for susceptibility for proteinuria in patients with type 2 diabetes
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rs2863389, rs7935082 and rs952635 implicated in type-2 diabetes by
normal increased risk of type-2 diabetes
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rs4655595 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.37 (CI 1.17-1.59), and for homozygotes, 2.33 (CI 1.23-4.42).
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rs7202877 is located at chromosome 16q23.1. in the intergenic region ~6 Kb upstream of CTBR2 and CTBR1, and ~54 Kb from BCAR1. This SNP has been associated with increased risk for type-1 diabetes and type-2 diabetes . Diabetes is a disease that affects how the body metabolizes glucose, and is characterized by high levels of glucose in the blood. Overtime, this can cause serious health problems in the eyes, kidneys, heart, nerves and teeth. Meanwhile, insulin is a hormone that helps the cells to uptake glucose for energy. There are two types of diabetes: type 1 and type 2. In type 1 diabetes, the pancreas does not produce insulin. The main factors contributing to the development of this type of diabetes are genetics and exposure to certain viruses . In type 2 diabetes, the pancreas does not...
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[GWAS:Type 2 diabetes]
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A study of 10572 African American and Hispanic American subjects linking genetics, magnesium intake and ethnicity Genetic Variations in Magnesium-Related Ion Channels May Affect Diabetes Risk among African American and Hispanic American Women suggests a link (OR = 0.84, false discovery rate (FDR)-adjusted P = 0.02) between rs6584273 in CNNM1 and T2D risk in African American women. Association between in vivo alcohol metabolism and genetic variation in pathways that metabolize the carbon skeleton of ethanol and NADH reoxidation in the Alcohol Challenge Twin Study
Frequency: 88.5%
References:1
References:1
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[GWAS:Type 2 diabetes]
Frequency: 91.2%
References:1
References:1
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Allele G associated with 1.21x risk of Type 2 Diabetes in study of 17,492 Han Chinese and Asian control group . As (A,A) is the rare variant, it thus effectively reduces risk. In slight Linkage Disequilibrium with rs5945326 near DUSP9 gene, forming a single locus. [GWAS:Type 2 diabetes]
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[GWAS:Type 2 diabetes]
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rs1007888(C;C) was associated with an increased risk of type-2 diabetes in women [hazard ratio (95% CI) 1.74 (1.02-2.97)], but not in men [1.17 (0.75-1.81)]. Macrophage migration inhibitory factor in acute lung injury: expression, biomarker, and associations. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. The macrophage migration inhibitory factor (MIF) gene polymorphism in Czech and Russian patients with myocardial infarction. Macrophage migration inhibitory factor: critical role in obesity, insulin resistance, and associated comorbidities. Usefulness of Mendelian randomization in observational epidemiology.
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rs1801262 increases susceptibility to Type II Diabetes 1.15 times for carriers of the A allele Mutation of CERKL, a novel human ceramide kinase gene, causes autosomal recessive retinitis pigmentosa (RP26). NeuroD1 gene and interleukin-18 gene polymorphisms in type 1 diabetes in Dalmatian population of Southern Croatia. Identification of type 2 diabetes-associated combination of SNPs using support vector machine.
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[GWAS:Type 2 diabetes]
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rs2073658 a borderline association with metabolic syndrome was observed (p = 0.036, IDF), the minor allele being the risk-increasing allele. The minor allele of rs2073658 also associated with higher total and LDL-cholesterol, apolipoprotein B-100 and lipoprotein(a) concentrations in longitudinal analyses. rs2073658 is associated with a modestly increased risk to develop type 2 diabetes in Dutch Caucasians, with considerable impact at the population level. [OMIM:HYPERLIPIDEMIA, FAMILIAL COMBINED, SUSCEPTIBILITY TO]
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nature type-2 diabetes *rs2237895, P = 7.3 times 10-9; OR = 1.32, 95% CI = 1.20–1.45 SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. Meta-analysis in genome-wide association studies. Genetic variation in KCNQ1 associates with fasting glucose and beta-cell function: a study of 3,734 subjects comprising three ethnicities living in Singapore. Common variants in KCNQ1 are associated with type 2 diabetes and impaired fasting glucose in a Chinese Han population. Polymorphisms in KCNQ1 are associated with gestational diabetes in a Korean population. KCNQ1 gene polymorphisms are associated with lipid parameters in a Chinese Han population. Variants in KCNQ1 increase type II diabetes susceptibility in South Asians: a stu...
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Associated with diabetic nephropathy and type-2 diabetes in a Japanese population.
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[PharmGKB:Non-Curated GWAS results: SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. (Initial Sample Size: 194 Japanese cases, 1,558 Japanese controls; Replication Sample Size: 4,924 cases, 2,618 controls (Japanese), 1433 cases, 1,735 controls (Singaporean), 3,891 cases, 4,888 controls (Danish)); (Region: 6p22.3; Reported Gene(s): CDKAL1; Risk Allele: rs4712524-G); (p-value= 0.0000000003).This variant is associated with Type 2 diabetes.] [GWAS:Type 2 diabetes]
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equivalent to rs10946398 and rs4712523 and implicated in type-2 diabetes
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rs1143699, rs4807015, and rs1978237 confer an increased risk of developing type-2 diabetes
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rs1113132 increases susceptibility to Type II Diabetes 1.15 times for heterozygotes (CG) and 1.36 times for homozygotes (CC)
normal
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rs1495377 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.28 (CI 1.11-1.49), and for homozygotes, 1.51 (CI 1.28-1.78). Note: orientation of this SNP is presumed correct but should be confirmed [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,924 cases, 2,938 controls; Replication Sample Size: (see Zeggini 2007); Risk Allele: rs1495377-G). This variant is associated with type 2 diabetes.] [GWAS:None] [GWAS:Type 2 diabetes]
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rs1884613 associated with type-2 diabetes in a Scandinavian population
normal
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rs17036314 is a SNP in the peroxisome proliferator-activated receptor gamma PPARG gene. In a 4 year study of 479 overweight individuals with impaired glucose tolerance (IGT) who participated in the Finnish Diabetes Prevention Study (DPS), carrying a rs17036314(C) allele predicted conversion to type-2 diabetes (T2D) after adjustment for baseline fasting glucose (p=0.030). Increased physical activity reduced this risk.
if diabetic, better response to rosiglitazone
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A total of 262 Korean type-2 diabetes patients were treated with 12 weeks of rosiglitazone at 4mg/day and genotyped to reveal that rs10192566(G) allele carriers responded better than (C) carriers. Patients with rs10192566(G) alleles had a larger decrease in fasting plasma glucose, 2-h postprandial glucose, and HbA1c than rs10192566(C;C) homozygotes. None of the other LPIN1 gene SNPs tested were associated with response. Note: rs11693809, rs10192566, and rs2278513 are in nearly complete linkage disequilibrium (D'>0.958, r(2) >0.882). [PharmGKB:Curated A study in patients with type 2 diabetes treated with rosiglitazone showed that this SNP in the LPIN1 gene was significantly associated with rosiglitazone treatment response. rs11693809 and rs2278513 are in nearly complete linkage diseq...
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news rs35463555 and rs17373080, associated nominally with type-2 diabetes. The rs17373080 C allele displayed higher basal transcription activity (P value <0.05). The DNA-mobility shift assay indicated that oligonucleotides corresponding to either rs17373080 allele bound NF1 transcription factors in whole cell extracts to the same extent.
normal fat metabolism; common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
normal risk
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rs1859962 is a SNP on chromosome 17q24.3, associated with increased risk for prostate cancer in several studies. In a study of over 3,600 Caucasians with prostate cancer, rs1859962 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On its own, the rs1859962(G;G) risk genotype yields an odds ratio for developing prostate cancer of 1.28 (CI: 1.11-1.47, p=5.5x10e-4) and may account for 6.5% of population attributable risk. news linked to Prostate cancer and type-2 diabetes cancer-genetics these snps influence genetic risk for prostate cancer *the haplotype rs6983267 rs1016343 rs4242384 *rs7501939 *rs1859962 *rs2660753 *rs9364554 *rs6465657 *rs10993994 *rs7931342 *rs2735839 *rs5945619 *rs10993994 [PharmGKB:Curated GWAS Results: Two variants ...
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rs1121980, a SNP in the FTO gene, showed the strongest association of several SNPs in the region with early onset obesity in a study of ~1,000 Caucasians. The odds ratio for the rs1121980(T) risk allele was 1.66 (CI: 1.37–2.01); and the odds ratios for heterozygotes and homozygotes (rs1121980(T;T)) were estimated (with a correct p<0.0001) at 1.67 (CI: 1.22–2.27) and 2.76 (CI: 1.88–4.03), respectively. Note that although rs1121980 showed the strongest association, it is in a block in the FTO gene of at least 5 other SNPs that are in linkage disequilibrium (r<sup>2</sup>>=0.88 for all). The other 5 SNPs are: * rs9939973 * rs7193144 * rs9940128 * rs8050136 * rs9939609 This SNP is also associated with (severe) obesity i...
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This snp influences obesity however the most strongly linked neighboring snp is rs9939609. You probably want that one. This plos genetics paper reports rs9930506 showed the strongest association with BMI (p = 8.6 *10-7), hip circumference (p = 3.4 * 10-8) and weight (p = 9.1 * 10-7). homozygotes for the rare 'G' allele were were 1.3 BMI units heavier than homozygotes for the common 'A' allele. This SNP did not show any association with obesity, type-2 diabetes or any other related traits in a study of 3,210 Chinese subjects. Furthermore, the minor allele frequency was much lower in Chinese populations compared to populations of European descent. rs9930506 (A;A) showed decreased levels of methylated PPARGC1A in comparison with AG + GG genotypes, suggesting a potential role of promoter PPARG...
normal
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This SNP is in a linkage block in the FTO gene with rs1121980; see rs1121980 for the association of this block with early onset obesity since it showed the strongest association. This SNP did not show any association with obesity, type-2 diabetes or any other related traits in a study of 3,210 Chinese subjects. Furthermore, the minor allele frequency was much lower in Chinese populations compared to populations of European descent. However, a more recent study of 4,189 Chinese Han subjects combined with a meta-analysis of published studies concluded that rs8050136(A) was associated with both increased risk for type-2 diabetes and obesity. rs8050136 associated with increased food intake, but not of impaired energy expenditure. [PharmGKB:Non-Curated GWAS results: Genome-wide association yie...
common in clinvar
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suggested the contribution of rs237025 to type-1 diabetes, however in this failed to replicate. This SNP is also known as Met55Val, M55V, or A163G. This was the first SNP in SNPedia. The type 1 diabetes susceptibility gene SUMO4 at IDDM5 is not associated with susceptibility to rheumatoid arthritis or juvenile idiopathic arthritis. Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. Evidence for the role of small ubiquitin-like modifier 4 as a general autoimmunity locus in the Japanese population. SUMO4 M55V variant is associated with diabetic nephropathy in type 2 diabetes. Association study of NFKB1 and SUMO4 polymorphisms in Chinese patients with pso...
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The T allele of rs1260326 has been associated with type 2 diabetes and hypertriglyceridemia. A fine mapping approach indicates that this SNP, rs1260326, shows the strongest association signal with metabolic phenotypes in the region that also harbors the tightly linked (r(2)=0.93) SNP rs780094, which has been previously associated with triglyceride and glucose concentrations. This SNP, rs1260326, encodes a common missense glucokinase regulatory protein gene GCKR variant. gout association, based on Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. The common P446L polymorphi...
average
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rs780094, a SNP in the GCKR gene encoding the glucokinase regulatory protein, contributes to the risk of type-2 diabetes and dyslipidaemia in mulitple populations. The effect on type 2 diabetes is probably mediated through impaired beta cell function rather than through obesity. The rs780094(A) risk allele is associated with the following traits : * higher levels of fasting serum triacylglycerol * impaired fasting and OGTT-related insulin release * dyslipidemia * somewhat reduced risk of type-2 diabetes There may also be an additive effect between this SNP and a SNP known as 'GCK -30A', rs1799884, at least on fasting serum insulin levels. rs780094 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched norm...
Magnitude: 0
Frequency: 47.8%
References:23
Frequency: 47.8%
References:23
normal
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A study of 14,000 Indian Asian or Caucasian adults indicates that rs12970134(A) alleles are associated with obesity. The average increase in waist circumference is 0.9cm BMI units per risk allele. see also The common obesity variant near MC4R gene is associated with higher intakes of total energy and dietary fat, weight change and diabetes risk in women. Variants near MC4R are associated with obesity and influence obesity-related quantitative traits in a population of middle-aged people: studies of 14,940 Danes. Investigation of the locus near MC4R with childhood obesity in Americans of European and African ancestry. The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI. Large effects on body mass index and insulin resistanc...
Magnitude: 0
Frequency: 50.4%
Repute:Good
References:90
Frequency: 50.4%
Repute:Good
References:90
normal
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A study of 60,000 adults indicates that rs17782313(C) alleles are associated with higher body mass index (BMI), with even greater effect in children. The average increase in BMI is 0.22 BMI units (p = 2.8 x 10<sup>-15</sup>). Note that rs10871777 is considered an equivalent SNP in Caucasian and Asian populations. The rs17782313(C) allele is equivalent to the rs10871777(G) allele. The rs17782313](C) allele is significantly associated with higher intakes of total energy and dietary fat. In addition, the SNP was related to greater long-term weight change and increased risk of diabetes in women. rs17782313(C) more snacking, however rs1421085(C) did not influence eating behavior obesity and type-2 diabetes *rs1121980 *rs7498665 *rs4752856 *rs17782313 *rs2815752 *rs10938397 [PharmGK...
Magnitude: 0
Frequency: 51.8%
References:5
Frequency: 51.8%
References:5
normal
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rs11868035 is one of several SNPs associated with the SREBF1 gene that show a modest association with type-2 diabetes. A study of ~2,000 Caucasian patients (and 10,000+ controls) led to an odds ratio of 1.19 (CI: 1.07-1.33, p=0.002) for the minor (risk) allele, rs11868035(A), in the orientation as in dbSNP. type-2 diabetes rs2297508(C) and rs11868035(C) This SNP rs11868035 and rs1057217 are associated with increased risk of schizophrenia in German and Scandinavian samples. This SNP and rs6812193 are reported to affect risk of Parkinson's disease. plos Polymorphisms in the gene encoding sterol regulatory element-binding factor-1c are associated with type 2 diabetes. [PharmGKB:Curated This SNP in the SREBF1 gene was strongly associated with schizophrenia in German, Danish and Norwegian samp...
None
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Also known as I128T MTP rare allele of the MTP I128T polymorphism may be protective against impaired glucose tolerance, type-2 diabetes Association of polymorphisms in glutamate-cysteine ligase catalytic subunit and microsomal triglyceride transfer protein genes with nonalcoholic fatty liver disease. [OMIM:MICROSOMAL TRIGLYCERIDE TRANSFER PROTEIN, 88-KD; MTP]
common
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rs5370, also known as Lys198Asn or K198N, is a SNP in the endothelin-1 EDN1 gene on chromosome 6. The generally more common rs5370(G) allele encodes the Lys (K), and the rarer rs5370(T) allele encodes the Asn (N). Among the French-Canadian founder population of the Saguenay Lac St-Jean region of Quebec, rs5370(T) was associated with lower HDL cholesterol values in women (p = 1.3 x 10e-5), but not in men. In a study of 1,000+ Western Australians, no association was seen between HDL levels and rs5370. A study of ~400 rheumatoid arthritis patients found a 3x increase in the adjusted odds of being hypertensive for rs5370(T;T) homozygotes compared to (G;G) homozygotes (odds ratio 2.89, CI: 1.02 - 8.19, p=0.011). After adjustment for multiple potential confounders, haplotype analysis revealed an...
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rs1053049, rs6902123, and rs2267668 in PPARD affect Lifestyle Intervention induced changes in overall adiposity, hepatic fat storage, and relative muscle mass. Our findings provide a mechanistic explanation for the involvement of these genetic variations in the development of insulin resistance and type-2 diabetes. [OMIM:PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR-GAMMA, COACTIVATOR 1, ALPHA;]
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Implicated in type-2 diabetes based on a study of 1,161 Finnish patients.
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associated with type-2 diabetes
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associated with type-2 diabetes
common in complete genomics
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nature type-2 diabetes *rs2283228 (additive model P = 3.1 times 10-12; OR = 1.26, 95% CI = 1.18–1.34). [OMIM:DIABETES MELLITUS, NONINSULIN-DEPENDENT; NIDDM]
common in complete genomics
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23andMe blog rs2237892(C) is associated with an increased risk for developing type-2 diabetes. each C at rs2237892 increased the odds of type 2 diabetes by 1.4 times, compared to the TT genotype. It’s important to note, however, that the C version is actually pretty common. In Asian populations, the C version of rs2237892 increased a person’s odds of type 2 diabetes by 1.42 times compared to people with TT. But because about 50% of the Asian population is actually CT at this SNP, it could be viewed that CC has 1.3 times the odds compared to typical, while TT has 0.61 times the typical odds. In European populations, about 85% of people are CC. This means that the results of Yasuda et al really show that compared to most Europeans, people with CT at rs22...
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:0
Frequency: 85.8%
Repute:Good
References:0
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577 African American individuals with type-2 diabetes T2DM-ESRD and 596 AA controls. *rs11964281 (nominal P = 0.000291, adjusted P = 0.0289)
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Originally reported to be associated with type-2 diabetes in a genome-wide association study; yet then reported not to be associated with either T2D or related metabolic traits in a large Danish population (ultimately 17,000 patients for the latter study). Type 2 diabetes whole-genome association study in four populations: the DiaGen consortium.
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Originally reported to be associated with type-2 diabetes in a genome-wide association study; yet then reported not to be associated with either T2D or related metabolic traits in a large Danish population (ultimately 17,000 patients for the latter study).
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rs1143699, rs4807015, and rs1978237 confer an increased risk of developing type-2 diabetes
normal risk
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rs1528133, a SNP in the TUB gene, was found in a study of 492 unrelated type-2 diabetes patients to have a significant effect on body mass index and thus obesity (1.54 kg/m(2), p= 0.006). When two populations were combined, totaling ~1200 patients, the risk allele (rs1528133(C) averaged an increase of 0.54 kg/m2 (CI: –0.19-1.26). Two additional TUB SNPs, rs2272382, and rs2272383, mapping to the 3' end of the gene showed similar associations and were in linkage disequilibrium with rs1528133. A follow-up study of 1,680 middle-aged Dutch women found that this allele, rs1528133(C), was significantly associated with increased weight (+1.88 kg, p=0.022) and body mass index (+0.56 units, p= 0.05). rs1528133(C) carriers were also associated with an increased glycemic load of 1.8...
common in complete genomics
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A search for variants associated with young-onset type 2 diabetes in American Indians in a 100K genotyping array.
common in complete genomics
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rs997509 increases the risk of Type-2 diabetes for the obese. *rs997509 we found a new SNP, rs997509, in intron 1 that is strongly associated with risk of type 2 diabetes in obese individuals. [PharmGKB:Curated A study of 809 children, 409 obese and 400 lean controls, conclude that the ENPP1 rs997509T allele can predispose obese children to metabolic syndrome and impaired glucose tolerance and that this variant might drive the association between the ENPP1 121Q allele and insulin resistance]
Magnitude: 0
Frequency: 92.3%
Repute:Good
References:6
Frequency: 92.3%
Repute:Good
References:6
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:3
Frequency: 98.2%
Repute:Good
References:3
common in complete genomics
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type 2 diabetes and fasting plasma glucose concentration.
common in clinvar
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rs268, also known as LPL '''Asn291Ser''' as well as '''LPL N291S''' or '''N318S''', a SNP in the lipoprotein lipase LPL gene, has been linked to increased susceptibility to hypertriglyceridemia, heart disease, Type-2 diabetes, idiopathic venous thromboembolism. A systematic review and meta-analysis of the relationship between lipoprotein lipase Asn291Ser variant and diseases. The summary standardized mean difference (SMD) of plasma triglyceride (TG) for carriers compared with noncarriers of the Asn291Ser variant was 3.23 (P < 0.00001). The summary SMD of plasma HDL-cholsterol (HDL-C) for carriers compared with noncarriers of the Asn291Ser variant was -3.42 (P < 0.0001). The summary SMD of the association of the Asn291Ser variant with plasma TG increased with increasing age and weight...
normal
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rs5219, also known as E23K, is a SNP in the KCNJ11 gene. The association between type-1 diabetes and rs5219 is mentioned as being replicated in ; there is also a 90% correlation between rs5219 and rs5215. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under an additive model, the odds ratio for the minor (risk) allele (T) is 1.15 (CI: 0.95-1.4, p=0.2, ie not significant). But for the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). Genotyping of ~4000 Chinese as well a meta-analysis concluded that rs5219 was associated with type-2 diabet...
normal
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The accuracy of claims about this snp are called into question by table 1 of discusses the process of including this snp into Coriell and raises some doubt about the value of its inclusion. rs7754840 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.28 (CI: 1.17-1.41, p = 4.5 x 10e-7) type-2 diabetes Carriers of the (C;G) and (C;C) genotypes of rs7754840 had 11% and 24% lower first-phase insulin release in an IVGTT compared to that in carriers of the (G;G) genotype (P=0.002). The C allele was also associated with higher glucose area under the curve in an OGTT (P=0.016). rs7754840 type-2 diabetes Ashkenazi Jewish population shows an even stronger effect for rs7754840 than the general Caucasian population, based on 1,131 cases versus 1,147 co...
171 snps
(hide) Tyrosinemia type I
Magnitude: 0
Frequency: 92.9%
Repute:Good
References:3
Frequency: 92.9%
Repute:Good
References:3
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[OMIM:FUMARYLACETOACETASE PSEUDODEFICIENCY]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Identification of a stop mutation in five Finnish patients suffering from hereditary tyrosinemia type I. Simple detection of a (Finnish) hereditary tyrosinemia type 1 mutation. [OMIM:?]
10 snps
(hide) Ulcer
normal
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. It is also known as M1V or Met1Val. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. Clopidogrel Efficacy [Pharm...
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
3 snps
(hide) Ulcerative colitis
1.33x increased risk of Ulcerative Colitis, but much lower Type 1 Diabetes risk. This raises the risk of Ulcerative Colitis (according to 23andMe), but also greatly lowers the risk of Type 1 Diabetes. It may also affect other autoimmune diseases.
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A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ancestry, concluded that this SNP and several others were associated with altered risk for the disease. [PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 6p21.32; Reported Gene(s): BTNL2, HLA-DRA, HLA-DRB5, HLA-DRB1, HLA-DQA1, HLA-DQB1; Risk Allele: rs2395185-?); (p-value= 0.0000000000000001).This variant is associated with Ulcerative colitis.] [OMIM:?] [GWAS:Ulcerative colitis]
1.5x increased risk for Crohn's disease; 2x increased risk for Graves' disease
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SNP rs2201841, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. Another study found that the 'A allele' and 'AA genotype' were significantly overrepresented in Graves' disease patients with Graves ophthalmopathy, based on 216 North American patients. The odds ratios reported were 2.04 for the allele (p=1x10<sup>-4</sup>), and for the so-called 'AA' genotype (presumably rs2201841(T;T) when correctly oriented to the dbSNP orientation), 2.4 (p=1x10<sup>-4</sup>). 23andMe blog psoriasis Europeans *rs2201841(G) 1.13x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication S...
Magnitude: 2
Frequency: 38.9%
Repute:Bad
References:40
Frequency: 38.9%
Repute:Bad
References:40
1.5x increased risk for certain autoimmune diseases; 2x increased risk for Graves disease
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SNP rs10889677, in the IL23R gene, is associated with increased risk for Crohn's disease in both Jewish and non-Jewish populations. The same risk allele for this SNP has been associated with increased risk for ankylosing spondylitis in a large study of over 1,000 Caucasian patients. The odds ratio is 1.3 (p=1.3x10e-6). In a study of 216 North American patients with Graves' disease, the C allele of rs10889677 was 2.03x overrepresented (p=1.3x10<sup>–4</sup>), and the homozygous rs10889677(C;C) genotype was also overrepresented (2.36x; p=1.4x10<sup>-4</sup>) in Graves ophthalmopathy patients. A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ance...
1.4x increased risk for Crohn's disease in Caucasians
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rs2241880, a SNP in the ATG16L1 gene encoding a threonine to alanine substitution ('T300A') in a protein known to be involved in the function of the epithelial cells lining the intestine, has been associated with Crohn's disease in several recent studies. In another recent (2007) report, rs2241880 is confirmed to be associated with both Crohn's disease and ileal disease, but additionally, the authors calculate risk for individuals who are homozygotes for this SNP plus 2 others (in the IBD5 and NOD2 genes). Individuals homozygous for the risk alleles for all 3 of these SNPs are estimated to be at 20 fold higher risk (CI ~9-49) for Crohn's disease. From the largest most recent survey, the Crohn's disease-associated SNPs for IBD5 and NOD2 are, respectively, rs6596075 and rs17221417. associate...
1.1x risk Crohn's Disease
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rs9858542 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.09 (CI 0.96-1.24), and for homozygotes, 1.84 (CI 1.49-2.26). [PharmGKB:Non-Curated GWAS results: Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: 1,182 cases, 2,024 controls). This variant is associated with Crohn's disease.] [OMIM:INFLAMMATORY BOWEL DISEASE 12; IBD12] [GWAS:Ulcerative colitis] [GWAS:Crohn's disease]
Magnitude: 1.1
Frequency: 91.8%
Repute:Bad
References:100
Frequency: 91.8%
Repute:Bad
References:100
Normal, but higher risk for certain autoimmune diseases. Almost everyone has this form, but it indicates a slightly higher risk of Ankylosing Spondylitis, Crohn's Disease (1.09x), Psoriasis (1.06x), and Ulcerative Colitis (1.06x). The risk is much greater than for the rare version. This is the interleukin-23 (IL-23) receptor. Media:http://www.the-rheumatologist.org/details/article/2528901/Neutralizing_IL-23_and_Its_Targets_May_Improve_Ankylosing_Spondylitis.html] Neutralizing IL-23 and Its Targets May Improve Ankylosing Spondylitis by Lara C. Pullen, PhD in The Rheumatologist newsmagazine ]
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A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-1....
Frequency: 1.8%
References:5
References:5
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[OMIM:?] [GWAS:None]
Frequency: 7.1%
References:2
References:2
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[GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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rs4728142, rs3807306 and a 5 bp insertion-deletion linked multiple sclerosis in three populations Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Exon expression in lymphoblastoid cell lines from subjects with schizophrenia before and after glucose deprivation. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus. Genetic risk factors in lupus nephritis and IgA nephropathy--no support of an overlap. Survival dimensionality reduction (SDR): development and clinical application of an innovative approach to detect epistasis in presence of right-cens...
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[PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 1p36.13; Reported Gene(s): RNF186; Risk Allele: rs3806308-?); (p-value= 0.000000007).This variant is associated with Ulcerative colitis.] [OMIM:INFLAMMATORY BOWEL DISEASE 7; IBD7] [GWAS:Ulcerative colitis]
Frequency: 15.9%
References:8
References:8
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[GWAS:Ulcerative colitis]
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[OMIM:?] [GWAS:Ulcerative colitis]
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[OMIM:?] [GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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[PharmGKB:Non-Curated Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. (Initial Sample Size: 1,167 cases, 777 controls; Replication Sample Size: 1,855 cases, 3,091 controls); (Region: 6p21.32; Reported Gene: HLA-DRA, BTNL2; Risk Allele: rs9268877-T) This variant is associated with Ulcerative colitis.] [OMIM:INFLAMMATORY BOWEL DISEASE 3; IBD3] [GWAS:Ulcerative colitis]
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A Danish case-control study comprising 373 Crohn's disease and 541 ulcerative colitis patients (and 796 healthy controls) concluded that carriers of the homozygous COX-2 and MDR1 intron 3 variant (rs3789243) had a relatively high risk of CD, odds ratio (95% CI) (OR (95% CI))=2.86 ((1.34-5.88) p=0.006) and 1.39 ((0.99-1.92) p=0.054), respectively, and for UC of 2.63 ((1.33-5.26) p=0.005) and 1.28 ((0.96-1.51) p=0.093), respectively, assuming complete dominance. [PharmGKB:Curated This variant maybe associated with drug resistance in chinese epilepsy patients. Sample size: 464 chinese epilepsy patients (270 drug responsive, 194 drug resistant).] [OMIM:ATP-BINDING CASSETTE, SUBFAMILY B, MEMBER 1; ABCB1]
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[GWAS:Ulcerative colitis]
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A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ancestry, concluded that this SNP and several others were associated with altered risk for the disease. [PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 1p36.13; Reported Gene(s): OTUD3, PLA2G2E; Risk Allele: rs6426833-G); (p-value= 0.0000000000005).This variant is associated with Ulcerative colitis.] [OMIM:INFLAMMATORY BOWEL DISEASE 7; IBD7] [GWAS:Ulcerative colitis]
Frequency: 24.8%
References:2
References:2
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[GWAS:Ulcerative colitis]
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Genetic analysis of innate immunity in Crohn's disease and ulcerative colitis identifies two susceptibility loci harboring CARD9 and IL18RAP. Elucidating the chromosome 9 association with AS; CARD9 is a candidate gene. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [GWAS:Ulcerative colitis]
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[OMIM:INFLAMMATORY BOWEL DISEASE 3; IBD3] [GWAS:Ulcerative colitis]
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Mapping the genetic architecture of gene expression in human liver. Association of MHC SNP genotype with susceptibility to type 1 diabetes: a modified survival approach. A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Quantitative trait loci for CD4:CD8 lymphocyte ratio are associated with risk of type 1 diabetes and HIV-1 immune control. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. D...
Frequency: 31.9%
References:5
References:5
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[OMIM:INFLAMMATORY BOWEL DISEASE 20; IBD20] [GWAS:Crohn's disease]
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A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ancestry, concluded that this SNP and several others were associated with altered risk for the disease. [PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 12q15; Reported Gene(s): IFNG, IL26, IL22; Risk Allele: rs1558744-A); (p-value= 0.000000000003).This variant is associated with Ulcerative colitis.] [OMIM:INFLAMMATORY BOWEL DISEASE 26; IBD26] [GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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[PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 7q31.1; Reported Gene(s): SLC26A3, DLD, LAMB1; Risk Allele: rs2158836-A); (p-value= 0.000007).This variant is associated with Ulcerative colitis.] [GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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associated with ulcerative colitis
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[GWAS:Ulcerative colitis]
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via spitoon reports about which identifies 32 snps relevant to Crohn's disease: '''Out of a possible total of 46, 80% of people will have between 17 and 25 copies of the riskier versions of these SNPs. Because there are so many of these SNPs--and because the riskier versions are often more common than their less risky counterparts--even people at the high end of the distribution are not much more likely than average to develop Crohn's disease.''' *rs3197999 A 1.2 *rs2188962 T 1.25 *rs2476601 G 1.31 *rs2274910 C 1.14 *rs9286879 G 1.19 *rs10045431 C 1.11 *rs6908425 C 1.21 *rs2301436 T 1.21 *rs1456893 A 1.2 *rs1551398 A 1.08 *rs10758669 C 1.12 *rs3764147 G 1.25 *rs2872507 A 1.12 *rs744166 A 1.18 *rs762421 G 1.13 *rs3763313 C 1.19 Proxy snps on 23andMe *rs7714584 G 1.33 *rs6478108 T 1.22 *rs12...
Frequency: 43.4%
References:2
References:2
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[GWAS:Ulcerative colitis]
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[PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 7q31.1; Reported Gene(s): Intergenic; Risk Allele: rs4730273-?); (p-value= 0.000005).This variant is associated with Ulcerative colitis.] [GWAS:Ulcerative colitis]
Frequency: 44.2%
References:6
References:6
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[OMIM:INFLAMMATORY BOWEL DISEASE 23; IBD23] [GWAS:Crohn's disease]
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[GWAS:None]
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[GWAS:Ulcerative colitis]
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[PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 7q31.1; Reported Gene(s): SLC26A3, DLD, LAMB1; Risk Allele: rs4598195-?); (p-value= 0.000001).This variant is associated with Ulcerative colitis.] [GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [GWAS:Crohn's disease]
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[GWAS:Ulcerative colitis]
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[PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 7q31.1; Reported Gene(s): SLC26A3, DLD, LAMB1; Risk Allele: rs4730276-?); (p-value= 0.000009).This variant is associated with Ulcerative colitis.] [GWAS:Ulcerative colitis]
normal
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rs2305480 is one of several SNPs from a region on chromosome 17q21 that has been linked to risk for asthma. A total of 651 French patients with asthma, from among 1,621 subjects in 388 families, were analyzed for SNPs in the (17q21) region. An association was found between this SNP and early-onset asthma (but not with later onset asthma) which was significant after correction at p < 0.001. Upon further study, this association was seen primarily only in children exposed to tobacco smoke. The odds ratio was 2.77, based on the most likely assumption that this risk is associated only with the recessive homozygous state (and not the heterozygous state, which is still possible). [PharmGKB:Curated This variant in the 17q21 region was strongly associated (P<0.001) with early-onset asthma. T...
Frequency: 51.8%
References:14
References:14
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[GWAS:Crohn's disease]
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[GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
Frequency: 55.8%
References:2
References:2
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[GWAS:None]
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rs8067378 is the strongest associating SNP from a region of chromosome 17q21 found in a large (ultimately over 7,000 patients in 3 populations) genome-wide association study of childhood asthma. Since the associated SNPs were also strongly associated (p < 10<sup>-22</sup>) in cis with transcript levels of from the ORMDL3 gene, the authors concluded that genetic variants regulating ORMDL3 expression are determinants of susceptibility to childhood asthma. Assessing the reproducibility of asthma candidate gene associations, using genome-wide data. Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene. Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in mexican children. Allele-specific chromatin remode...
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[GWAS:Ulcerative colitis]
normal risk of rheumatoid arthritis, SLE, Sjögren's syndrome, type-1 diabetes, and primary biliary cirrhosis.
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune dise...
Frequency: 61.9%
References:1
References:1
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[GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
Frequency: 70.8%
References:2
References:2
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[GWAS:None]
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[GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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[PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 9q21.32; Reported Gene(s): Intergenic; Risk Allele: rs668853-G); (p-value= 0.000002).This variant is associated with Ulcerative colitis.] [GWAS:Ulcerative colitis]
normal
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rs1143634, also known as +3954, is a SNP in the IL-1 beta IL1B gene. A study of 556 adults in the Western Australian coronary heart disease (CHD) population concluded that rs1143634(T;T) homozygotes had larger waist circumference, by 1.8cm on average, compared to major allele (C;C) homozygotes. This association was even more pronounced in patients with higher levels of obesity or inflammatory markers. rs1143634 increases susceptibility to Alopecia Areata 2.67 times for heterozygotes (CT) and 1.13 times for homozygotes (TT) rs1143634 increases susceptibility to Alzheimer's disease 2.33 times for homozygotes (TT) rs1143634 increases susceptibility to Cervical lesions, low-grade squamous intraepithelial lesions 4.29 times for heterozygotes (CT) and 3.57 times for homozygotes (TT) rs1143634 in...
common in complete genomics
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rs7524102 increases susceptibility to Bone mineral density variations, lower for carriers of the A allele rs7524102 increases susceptibility to Osteoporotic fractures 1.12 times for carriers of the A allele Common variants in the region around Osterix are associated with bone mineral density and growth in childhood. Replication study of candidate genes/loci associated with osteoporosis based on genome-wide screening. OPG and RANK polymorphisms are both associated with cortical bone mineral density: findings from a metaanalysis of the Avon longitudinal study of parents and children and gothenburg osteoporosis and obesity determinants cohorts. Analysis of recently identified osteoporosis susceptibility genes in Han Chinese women. [PharmGKB:Non-Curated GWAS results: New sequence variants ass...
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[PharmGKB:Non-Curated Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. (Initial Sample Size: 1,167 cases, 777 controls; Replication Sample Size: 1,855 cases, 3,091 controls); (Region: 1q32.1; Reported Gene: IL10; Risk Allele: rs3024505-T) This variant is associated with Ulcerative colitis.] [OMIM:INFLAMMATORY BOWEL DISEASE 23; IBD23] [GWAS:Ulcerative colitis]
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[GWAS:Ulcerative colitis]
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[OMIM:?] [GWAS:Ulcerative colitis]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 12q15; Reported Gene(s): IL26; Risk Allele: rs2870946-G); (p-value= 0.0000005).This variant is associated with Ulcerative colitis.] [OMIM:INFLAMMATORY BOWEL DISEASE 26; IBD26] [GWAS:Ulcerative colitis]
67 snps
(hide) Ureterolithiasis
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This SNP is reportedly associated with chronic kidney disease and kidney stones. [GWAS:None]
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DeCode reports that carriers of two T alleles at rs219778 have a slightly increased risk of developing kidney stones.
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23andMe blog each G at rs4293393 decreased the odds of chronic kidney disease by 24%. Approximately 18% of people with European ancestry have at least one G at this SNP. DeCode reports that the T allele of rs4293393 is associated with kidney stones and chronic kidney disease. This SNP may also be associated with susceptibility to gout], hypertension, and diabetes.
3 snps
(hide) Usher syndrome
References:6
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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The contribution of USH1C mutations to syndromic and non-syndromic deafness in the UK. [OMIM:?]
9 snps
(hide) Venous thromboembolism
higher risk of of coronary heart disease coronary heart disease
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rs662, also known as Q192R, is a SNP in the PON1 gene. It codes for amino acid 192 of the paraoxonase (PON) protein. Variants of this SNP affect PON catalytic efficiency and are correlated with Heart disease and trait-anxiety scores. The normal form, rs662(A), encodes a glutamine (Q), while the variant, rs662(G)), encodes an arginine (R). . While some populations show an association between this SNP and Heart disease, not all do. Perhaps the most striking finding was reported in Japanese patients with non-insulin dependent diabetes mellitus (NIDDM). NIDDM patients with either one or two rs662(G) alleles had a 9 fold higher risk of coronary heart disease compared with rs662(A;A) NIDDM patients. table of odds for cardiovascular disease outcomes 274 ovarian epithelial carcinoma cases and 452 ...
blood type O
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=Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women. |OA=23andMe blog each copy rs505922(C) is associated with 1.2x risk of pancreatic cancer influences ABO blood group [PharmGKB:Non-Curated GWAS results: Common susceptibility allele are unlikely to contribute as strongly as the FV and ABO loci to VTE risk: results from a GWAS approach. (Initial Sample Size: 419 cases, 1,228 controls; Replication Sample Size: 1,757 cases, 1,480 controls); (Region: 9q34.2; Reported Gene(s): ABO; Risk Allele: rs505922-C); (p-value= 0.000000000000004).This variant is associated with Venous thromboembolism.] [OMIM:?] [GWAS:Venous thromboembolism]
Frequency: 4.4%
References:1
References:1
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
Frequency: 16.5%
References:2
References:2
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. *rs13146272 in CYP4V2 (risk allele frequency, 0.64) OR 1.24 (95% CI, 1.11-1.37) for rs13146272 *rs2227589 in SERPINC1 (risk allele frequency, 0.10) OR 1.29 (95% CI, 1.10-1.49) for rs2227589 *rs1613662 in GP6 (risk allele frequency, 0.84) OR 1.15 (95% CI, 1.01-1.30) for rs1613662 A study of 453 VTE cases and 1,327 controls was able to replicate the 'mild effects' of this SNP on risk for VTE, however they felt that stronger associations were found between increased VTE risk and either the Factor V Leiden mutation (rs6025)or having blood types O or A2. An evaluation of candidate genes of inflammation and thrombosis in relation to the risk of venous thromboembolism: The W...
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[GWAS:Venous thromboembolism (gene x gene interaction)]
normal risk
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The rs5361 Ser128Arg variation in this gene, known as E-selectin, is linked to several thrombotic disorders. rs5361(C;C) homozygous carriers of the Ser128Arg allele are at a 4X higher risk for recurrent venous thromboembolism (VTE); heterozygous carriers are not at increased risk. .
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rs1799864(G), rs3025058(A) and rs662 were associated with increased risk, and rs1800775(A) with reduced risk of recurrent venous thromboembolism [PharmGKB:Curated Meta-analysis showed weak inverse association with coronary risk for the CETP:-629C>A, A allele.] [OMIM:HIGH DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS] [GWAS:HDL cholesterol]
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[GWAS:Venous thromboembolism]
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. per risk allele odds ratio *rs13146272 in CYP4V2 (risk allele frequency, 0.64) OR 1.24 (95% CI, 1.11-1.37) for rs13146272 *rs2227589 in SERPINC1 (risk allele frequency, 0.10) OR 1.29 (95% CI, 1.10-1.49) for rs2227589 *rs1613662 in GP6 (risk allele frequency, 0.84) OR 1.15 (95% CI, 1.01-1.30) for rs1613662 A study of 453 VTE cases and 1,327 controls was able to replicate the 'mild effects' of this SNP on risk for VTE, however they felt that stronger associations were found between increased VTE risk and either the Factor V Leiden mutation (rs6025)or having blood types O or A2. An evaluation of candidate genes of inflammation and thrombosis in relation to the risk of ve...
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[OMIM:?] [GWAS:None]
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[GWAS:Venous thromboembolism]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism]
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[GWAS:Venous thromboembolism]
Frequency: 41.6%
References:1
References:1
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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rs10935838, rs2046934, rs5853517, and rs6809699 venous thromboembolism lower risk of incident DVT/PE as compared to the reference haplotype H1 (odds ratio=0.50, 95% CI=0.27-0.93, p=0.028) [PharmGKB:Curated This SNP was used to tag the H2 haplotype to show association with peripherial arterial disease and coronary artery disease.]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
Frequency: 57.5%
References:1
References:1
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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A common variant of the ABO gene protects against hypertension in a Spanish population. Pharmacogenetic predictors of angiotensin-converting enzyme inhibitor-induced cough: the role of ACE, ABO, and BDKRB2 genes. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer. [PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: Mean angiotensin converting enzyme activity among subjects with the CC genotype at ABO-rs495828 was higher than the CA or AA. Carriage of the A allele is associated with the A blood group antigen. The mean ACE activity of the blood type A subjects was significantly lower th...
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
Frequency: 78.8%
References:1
References:1
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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[GWAS:Venous thromboembolism (gene x gene interaction)]
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rs10935838, rs2046934, rs5853517, and rs6809699 venous thromboembolism lower risk of incident DVT/PE as compared to the reference haplotype H1 (odds ratio=0.50, 95% CI=0.27-0.93, p=0.028)
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The T allele of this SNP is associated with higher risk of pancreatic cancer. Phosphodiesterase 8B gene variants are associated with serum TSH levels and thyroid function. Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. Genetic variants associated with Von Willebrand factor levels in healthy men and women identified using the HumanCVD BeadChip. [PharmGKB:Non-Curated GWAS results: Population-based genome-wide association studies reveal six loci influencing plasma levels of live...
normal
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Several SNPs in the VKORC1 gene have been linked to warfarin sensitivity, with perhaps the most common being this SNP rs9923231. Note that the orientation as published in scientific articles is often on the opposite strand compared to the orientation in dbSNP, so you will sometimes see it as a G>T snp. It is also known as *-1639G>A with the minus indicating that this is in an upstream promoter *3673 based on its position in GenBank accession number AY587020. *VKORC1*2. The main findings related to the treatment of venous thromboembolism (aka VTE; from hypercoagulability) with the blood thinner warfarin for this SNP are that carriers of the rs9923231(T) allele require significantly reduced doses of warfarin, and are (otherwise) at a higher risk of serious bleeding. Clinical studies de...
common on affy axiom data
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rs10935838, rs2046934, rs5853517, and rs6809699 venous thromboembolism lower risk of incident DVT/PE as compared to the reference haplotype H1 (odds ratio=0.50, 95% CI=0.27-0.93, p=0.028)
common in clinvar
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Compared with individuals without CCR5-Delta32 (a variation in another gene) or rs1799864(A), individuals with one or two copies of rs1799864(A) had a 58% lower risk of developing AIDS during the first 4 years after testing positive for HIV, a 19% lower risk during the subsequent 4 years, and no significant protection thereafter. No protective effect (ie no benefit) was seen for this SNP once AIDS had developed. rs1799864(G), rs3025058(A) and rs662 were associated with increased risk, and rs1800775(A) with reduced risk of recurrent venous thromboembolism [OMIM:HUMAN IMMUNODEFICIENCY VIRUS TYPE 1, RESISTANCE TO]
normal risk for VTE
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rs867186 is a SNP that can indicate haplotype H3 of the EPCR gene. The protein product of the EPCR gene activates a part of the anticoagulation pathway. While the rs867186(A) allele could indicate haplotypes H1, H2 or H4, the rs867186(G) allele distinctly tags (identifies) the H3 haplotype. While most groups studying EPCR H3 agree that it leads to increased soluble EPCR, and thus should theoretically lead to reduced risk for venous thromboembolism, different groups come to different conclusions about the effect in the populations each studies. Two find no association while one finds that the H3 haplotype (and thus rs867186(G)) actually increases the risk of venous thromboembolism (VTE), with an odds ratio of 1.80, p=0.004. [GWAS:Plasma coagulation factors]
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
common in clinvar
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rs268, also known as LPL '''Asn291Ser''' as well as '''LPL N291S''' or '''N318S''', a SNP in the lipoprotein lipase LPL gene, has been linked to increased susceptibility to hypertriglyceridemia, heart disease, Type-2 diabetes, idiopathic venous thromboembolism. A systematic review and meta-analysis of the relationship between lipoprotein lipase Asn291Ser variant and diseases. The summary standardized mean difference (SMD) of plasma triglyceride (TG) for carriers compared with noncarriers of the Asn291Ser variant was 3.23 (P < 0.00001). The summary SMD of plasma HDL-cholsterol (HDL-C) for carriers compared with noncarriers of the Asn291Ser variant was -3.42 (P < 0.0001). The summary SMD of the association of the Asn291Ser variant with plasma TG increased with increasing age and weight...
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Risk of Placental Abruption and Venous Thromboembolism according to 23andMe The publicly-recognized name for this SNP is rs1799963. Oral Contraceptives, HRT and Risk of VTE
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23andMe blog relevant for blood transfusion compatibility. venous thromboembolism, [OMIM:SOLUTE CARRIER FAMILY 44, MEMBER 2; SLC44A2]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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[OMIM:?]
62 snps
(hide) Vitamin D Insufficiency
somewhat lower vitamin D levels
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rs2282679, located in the group-specific component (vitamin D binding protein) GC gene on chromosome 4p12, has been linked by several studies to vitamin D serum concentrations. In both studies, the allele associated with lower vitamin D, and thus the potential for vitamin D insufficiency, is rs2282679(C). Carriers of two such alleles have lower vitamin D than carriers of one allele, who in turn on average have lower vitamin D levels than rs2282679(A;A) individuals. A near-perfect proxy (i.e. substitute) for rs2282679 is reported to be rs4588. [GWAS:Vitamin D levels]
1 snp
(hide) Vitiligo
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23andMe blog rs1393350 A 1.29 Melanoma rs1393350 increases susceptibility to Blond rather than brown hair 1.29 times for carriers of the A allele rs1393350 increases susceptibility to Blue rather than green eyes 1.52 times for carriers of the A allele rs1393350 increases susceptibility to Skin sensitivity to sun 1.26 times for carriers of the A allele A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Digital quantification of human eye color highlights genetic association of three new loci. [OMIM:TYROSINASE; TYR] [GWAS:Tanning]
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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. [GWAS:Vitiligo]
Frequency: 16.8%
References:1
References:1
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[GWAS:Vitiligo]
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Generalized Vitiligo [OMIM:?] [GWAS:Vitiligo]
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[GWAS:Vitiligo]
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Celiac Disease [GWAS:Vitiligo]
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[OMIM:?] [GWAS:Vitiligo]
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Generalized Vitiligo
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Generalized Vitiligo [GWAS:Vitiligo]
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[OMIM:?] [GWAS:Vitiligo]
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[GWAS:Vitiligo]
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linked to generalized vitiligo Individuals carrying high-risk alleles of both rs6502867 and rs2670660 had an odds ratio of 4.20 compared with individuals carrying a high-risk allele from only one signal.
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[GWAS:Vitiligo]
Frequency: 45.1%
References:6
References:6
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[GWAS:Type 1 diabetes]
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[OMIM:?] [GWAS:Vitiligo]
Frequency: 46.9%
References:6
References:6
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[GWAS:Vitiligo]
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rs231775, also known as +49A/G, is a SNP in the CTLA4 gene. which is linked to Hashimoto thyroiditis In a meta-analysis of CTLA4 gene SNPs, rs231775 was most associated with vitiligo; however, the association seems to hold only in the subgroup of patients with other autoimmune diseases. rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease associated with the development of placental abruption and preeclampsia, with women having the G allele being at risk rs231775 was not associated with type-1 diabetes in a study of 207 Portuguese patients. [PharmGKB:Curated This SNP affects risk for Autoimmune Thyroid Disorder (AITD). The G allele is generally thought to be the risk-conferring allele, but this study found that which allele confers ri...
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Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. Shared and distinct genetic variants in type 1 diabetes and celiac disease. Investigation of type 1 diabetes and coeliac disease susceptibility loci for association with juvenile idiopathic arthritis. [PharmGKB:Non-Curated GWAS Results: Newly identified genetic risk variants for celiac disease related to the immune response (Initial Sample Size: 767 cases, 1,422 controls; Replication Sample Size: 1,643 cases, 3,406 controls; Risk Allele: rs1464510-A).] [OMIM:CELIAC DISEASE, SUSCEPTIBILITY TO, 11; CELIAC11] [GWAS:Celiac disease] [GWAS:Celiac disease]
Frequency: 51.3%
References:1
References:1
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Generalized Vitiligo
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[GWAS:Vitiligo]
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[GWAS:Vitiligo]
2.96x
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linked to generalized vitiligo Individuals carrying high-risk alleles of both rs6502867 and rs2670660 had an odds ratio of 4.20 compared with individuals carrying a high-risk allele from only one signal. Identification of intergenic trans-regulatory RNAs containing a disease-linked SNP sequence and targeting cell cycle progression/differentiation pathways in multiple common human disorders. Genetic association of NALP1 with generalized vitiligo in Jordanian Arabs. Genetic predictors of glucocorticoid response in pediatric patients with inflammatory bowel diseases. NLRP1 influences the systemic sclerosis phenotype: a new clue for the contribution of innate immunity in systemic sclerosis-related fibrosing alveolitis pathogenesis.
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Vitiligo http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000523 OR = 1.18, 95% CI = 1.06–1.32
Magnitude: 0
Frequency: 57.5%
References:1
Frequency: 57.5%
References:1
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[GWAS:Vitiligo]
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[GWAS:Vitiligo]
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[GWAS:Vitiligo]
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
27 snps
(hide) Von Willebrand disease
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rs1800386 Von Willebrand disease type 1
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rs121964895 Von Willebrand disease
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rs61748511 Von Willebrand disease
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rs121964894 Von Willebrand disease
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rs61750579 Von Willebrand disease
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rs62643630 Von Willebrand disease
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rs267607353 Von Willebrand disease
References:1
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rs61750591, also known as c.4944delT, p.Ile1649Serfs and p.1648fsX45, is a SNP in the VWF gene on chromosome 12. The rarer rs61750591(-) deletion allele is considered likely to cause Von Willebrand disease, type 1, according to one publication. This SNP appears to be referred to as i5039448 by 23andMe.
normal
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rs7639618 is one of several SNPs in the DVWA gene found to be associated with osteoarthritis based on a study of several Japanese patient populations. The allelic odds ratio is 1.45 (CI: 1.27-1.65, p = 2.2 x 10e-8) for the minor allele, which is the (T) allele (in dbSNP orientation). Our results suggest that the effect that DVWA amino acid changes have on tubulin binding is unlikely to influence risk of OA in Caucasians. rs7639618 with knee osteoarthritis with an odds ratio (OR) of 1.29, 95% confidence interval (CI) of 1.15 -1.45 and P of 2.70x10(-5), but not for Europeans [OMIM:OSTEOARTHRITIS SUSCEPTIBILITY 6; OS6]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common/normal
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rs33978901, also known as c.2771G>A, p.Arg924Gln and R924Q, is a SNP in the VWF gene on chromosome 12. The rarer rs33978901(T) allele (in dbSNP and SNPedia orientation) leads to reductions in VWF and FVIII levels particularly in combination with blood group O. Its inheritance alone may be insufficient for the diagnosis of Von Willebrand disease, but it does appear to be associated with a further VWF level reduction in individuals with a second VWF mutation and it also contributes to population variance in VWF and FVIII levels according to a 2010 publication. This SNP is referred to as i5049145 by 23andMe.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs41276738, also known as c.2561G>A, p.Arg854Gln and R854Q, is a SNP in the VWF gene on chromosome 12. The rare rs41276738(T) allele (in SNPedia orientation) is considered pathogenic for Von Willebrand disease, type 1, according to ClinVar and the VWFdb. This SNP is also referred to as i5049144 by 23andMe. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61748477, also known as c.2372C>T, Thr791Met and T791M, is a SNP in the VWF gene on chromosome 12. The rare rs61748477(T) allele is considered pathogenic for Von Willebrand disease, type 2N, according to ClinVar and the VWFdb. This SNP is also referred to as i5049057 by 23andMe. [OMIM:?]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs61748478, also known as c.2384A>G, p.Tyr795Cys and Y795C, is a SNP in the VWF gene on chromosome 12. The rare rs61748478(G) allele is considered pathogenic for Von Willebrand disease, type 2N, according to ClinVar and the VWFdb. This SNP is also referred to as i5049289 by 23andMe.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common/normal
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rs61748495, also known as c.3108+5G>A, is a SNP in the VWF gene on chromosome 12. The rarer rs61748495(A) allele is considered likely to cause Von Willebrand disease, type 1, according to one publication.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs61748497, also known as c.3178T>C, p.Cys1060Arg and C1060R, is a SNP in the VWF gene on chromosome 12. The rare rs61748497(C) allele is considered pathogenic for Von Willebrand disease, type 2N, according to ClinVar and the VWFdb.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61749372, also known as c.3814T>C, p.Cys1272Arg and C1272R, is a SNP in the VWF gene on chromosome 12. The rare rs61749372(C) allele is considered pathogenic for Von Willebrand disease, type 2A, according to ClinVar and the VWFdb. This SNP is also referred to as i5049192 by 23andMe. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61749380, also known as c.3854C>T, p.Ser1285Phe and S1285F, is a SNP in the VWF gene on chromosome 12. The rare rs61749380(T) allele is considered pathogenic for Von Willebrand disease, type 2M, according to ClinVar and the VWFdb. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61749384, also known as c.3916C>T, p.Arg1306Trp and R1306W, is a SNP in the VWF gene on chromosome 12. The rare rs61749384(C) allele is considered pathogenic for Von Willebrand disease, type 2B, according to ClinVar and the VWFdb. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61749387, also known as c.3922C>T, p.Arg1308Cys and R1308C, is a SNP in the VWF gene on chromosome 12. The rare rs61749387(T) allele is considered pathogenic for Von Willebrand disease, type 2B, according to ClinVar and the VWFdb. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61749397, also known as c.3946G>A, p.Val1316Met and V1316M, is a SNP in the VWF gene on chromosome 12. The rare rs61749397(A) allele is considered pathogenic for Von Willebrand disease, type 2B, according to ClinVar and the VWFdb. This SNP is also referred to as i5049165 by 23andMe. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61749398, also known as c.3970G>A, p.Gly1324Ser and G1324S, is a SNP in the VWF gene on chromosome 12. The rare rs61749398(A) allele is considered pathogenic for Von Willebrand disease, type 2M, according to ClinVar and the VWFdb. This SNP is also referred to as i5049157 by 23andMe. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61749403, also known as c.4022G>A, p.Arg1341Gln and R1341Q, is a SNP in the VWF gene on chromosome 12. The rare rs61749403(A) allele is considered pathogenic for Von Willebrand disease, type 2B, according to ClinVar and the VWFdb. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61750101, also known as c.4541T>G, p.Phe1514Cys and F1514C, is a SNP in the VWF gene on chromosome 12. The rare rs61750101(G) allele is considered pathogenic for Von Willebrand disease, type 2A, according to ClinVar and the VWFdb. This SNP is also referred to as i5049343. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61750117, also known as c.4789C>T, p.Arg1597Trp and R1597X, is a SNP in the VWF gene on chromosome 12. The rare rs61750117(T) allele is considered pathogenic for Von Willebrand disease, type 2A, according to ClinVar and the VWFdb. This SNP is referred to as i5049117 by 23andMe. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61750581, also known as c.4837T>C, p.Ser1613Pro and S1613P, is a SNP in the VWF gene on chromosome 12. The rare rs61750581(C) allele is considered pathogenic for Von Willebrand disease, type 2A, according to ClinVar and the VWFdb. This SNP is also referred to as i5049172 by 23andMe. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61750584, also known as c.4883T>C, p.Ile1628Thr and I1628T, is a SNP in the VWF gene on chromosome 12. The rare rs61750584(C) allele is considered pathogenic for Von Willebrand disease, type 2A, according to ClinVar and the VWFdb. This SNP is also referred to as i5049076 by 23andMe. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61750612, also known as c.5557C>T, p.Arg1853Ter, R1852X and R1853X, is a SNP in the VWF gene on chromosome 12. The rare rs61750612(T) allele is considered pathogenic for Von Willebrand disease, type 3, according to ClinVar and the VWFdb, at least when homozygous or compound heterozygous. It is possible that on it's own this allele leads to Type 1 Von Willebrand disease. This SNP is also referred to as i5049228 by 23andMe. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61750630, also known as c.7085G>T, p.Cys2362Phe and C2362F, is a SNP in the VWF gene on chromosome 12. The rare rs61750630(T) allele is considered pathogenic for Von Willebrand disease, type 3, according to ClinVar and the VWFdb. This SNP is also referred to as i5049314 by 23andMe. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common/normal
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rs61753993, also known as c.422A>G, p.Asp141Gly and D141G, is a SNP in the VWF gene on chromosome 12. The rarer rs61753993(G) allele is considered likely to cause Von Willebrand disease, type 1, according to one publication. This SNP is referred to as i5049208 by 23andMe.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs61754002, also known as c.1071C>A, p.Tyr357Ter and Y357X, is a SNP in the VWF gene on chromosome 12. The rare rs61754002(A) allele is considered pathogenic for Von Willebrand disease, type 2N, according to ClinVar and the VWFdb. This SNP is also referred to as i5049284 by 23andMe.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs61754010, also known as c.1583A>G, p.Asn528Ser and N528S, is a SNP in the VWF gene on chromosome 12. The rare rs61754010(G) allele is considered pathogenic for Von Willebrand disease, type 2A, according to ClinVar and the VWFdb.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs61754011, also known as c.1648G>A, p.Gly550Arg and G550R, is a SNP in the VWF gene on chromosome 12. The rare rs61754011(A) allele is considered pathogenic for Von Willebrand disease, type 2A, according to ClinVar and the VWFdb. This SNP is also referred to as i5049159 by 23andMe. [OMIM:?]
normal
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rs11718863 is one of several SNPs in the DVWA gene found to be associated with osteoarthritis based on a study of several Japanese patient populations. The allelic odds ratio is 1.43 (CI: 1.26-1.63, p = 5.2 x 10e-8) for the minor allele, which is the (T) allele (in dbSNP orientation). Association of the DVWA and GDF5 polymorphisms with osteoarthritis in UK populations. Large replication study and meta-analyses of DVWA as an osteoarthritis susceptibility locus in European and Asian populations. [OMIM:OSTEOARTHRITIS SUSCEPTIBILITY 6; OS6]
common in clinvar
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rs61749392, also known as c.3939G> C, p.Trp1313Cys and W1313C, is a SNP in the VWF gene on chromosome 12. The rare rs61749392(C) allele is considered pathogenic for Von Willebrand disease, type 2B, according to ClinVar and the VWFdb. This SNP is also referred to as i5049327 by 23andMe. [OMIM:?]
35 snps
(hide) Wilson's disease
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Mutation analysis and the correlation between genotype and phenotype of Arg778Leu mutation in chinese patients with Wilson disease.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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The Wilson disease gene: spectrum of mutations and their consequences. Mutation analysis in patients of Mediterranean descent with Wilson disease: identification of 19 novel mutations. Molecular pathogenesis of Wilson and Menkes disease: correlation of mutations with molecular defects and disease phenotypes. [OMIM:?]
12 snps